Atac-array for prediction of disease-free survival in pancreatic cancer

Abstract

The present disclosure relates to an array-based assay for transposase-accessible chromatin and prognostic molecular markers of treatment-resistant/early recurrent cancer. The present disclosure also relates to predicting an outcome, such as duration of disease-free survival, in a cancer patient.

1 . A method for predicting an outcome for a patient, the method comprising:
 a) providing a biological sample obtained from a treatment-naïve patient having, or suspected of having, cancer, said biological sample comprising morphologically intact nuclei from cells of the patient;   b) assessing chromatin accessibility of a first group of differentially accessible chromatin regions in the sample to obtain a first epigenetic signature value, wherein accessibility of said first group of differentially accessible chromatin regions is associated with a good prognosis;   c) optionally, assessing chromatin accessibility of a second group of differentially accessible chromatin regions in the sample to obtain a second epigenetic signature value, wherein accessibility of said second group of differentially accessible chromatin regions is associated with a poor prognosis; and   d) predicting the outcome based on (i) the the first epigenetic signature value and/or (ii) the relative difference between the first epigenetic signature value and the second epigenetic signature value, wherein the outcome is optionally responsiveness to a treatment modality and/or duration of disease-free survival.   
     
     
         2 . The method of  claim 1 , wherein at least one of step (b) or step (c) comprises a microarray-based hybridization reaction for transposase-accessible chromatin. 
     
     
         3 . The method of  claim 1  or  claim 2 , further comprising the steps of comparing the first epigenetic signature value to the second epigenetic signature value to obtain a differential value and, optionally, normalizing the differential value with a control value. 
     
     
         4 . The method of  claim 1 , wherein the method comprises determining a prognosis score (PS), wherein the PS is determined from at least the first epigenetic signature value and normalized by the difference between a positive and a negative control. 
     
     
         5 . The method of  claim 4 , wherein step (d) further comprises taking into account nuclear localization of a transcription factor, preferably HNF1b. 
     
     
         6 . The method of  claim 1  or  claim 2  or  claim 3 , further comprising predicting a long duration of disease-free survival when the first epigenetic value is significantly higher than the second epigenetic value and/or predicting a short duration of disease-free survival when the second epigenetic value is significantly higher than the first epigenetic value. 
     
     
         7 . The method of  claim 1  or  claim 2  or  claim 3 , wherein step (b) and/or step (c) comprise:
 i. contacting the intact nuclei to a transposase complex to produce a population of tagged DNA fragments representing accessible chromatin regions (ACRs) of the intact nuclei; 
 ii. attaching a detectable label to the tagged DNA fragments to produce labeled fragments; and 
 iii. contacting the labeled fragments to a set of oligonucleotides probes, wherein said set of oligonucleotide probes are bound to a solid support 
 
     
     
         8 . The method of any one of the preceding claims, wherein step (b) and step (c) are performed substantially simultaneously. 
     
     
         9 . The method of any one of the preceding claims, wherein the method does not include sequencing the tagged fragments or amplicons thereof. 
     
     
         10 . The method of any one of the preceding claims, wherein the patient has or is suspected of having malignant cancer. 
     
     
         11 . The method of any one of the preceding claims, wherein the patient has or is suspected of having pancreatic cancer. 
     
     
         12 . The method of any one of the preceding claims, wherein the biological specimen is a biopsy sample, preferably a fine needle biopsy sample, or a bodily fluid sample that contains cancer cells. 
     
     
         13 . The method of any one of the preceding claims, wherein said first group of differentially accessible chromatin regions comprises one or more, preferably two or more, or more preferably fifty or more, chromatin regions selected from  FIG. 9A  and/or said second group of differentially accessible chromatin regions comprises one or more, preferably two or more, or more preferably fifty or more, chromatin regions selected from  FIG. 9B . 
     
     
         14 . A solid support comprising a set of oligonucleotide probes bound thereto,
 wherein the set of oligonucleotide probes comprises a plurality of unique oligonucleotide probes,   wherein each unique oligonucleotide probe is hybridizable to a different chromatin region selected from the list of chromatin regions in  FIG. 9A  of  FIG. 9B  or a complement thereof, and   wherein the set of oligonucleotide probes collectively targets at least two, alternatively at least five, at least ten, at least twenty-five, at least fifty, at least one hundred, at least one hundred fifty, at least two hundred, at least two hundred fifty, at least three hundred, at least three hundred fifty, at least four hundred, at least four hundred fifty, at least five hundred, at least five hundred fifty, at least six hundred, at least six hundred fifty, at least seven hundred, at least seven hundred fifty, at least eight hundred, at least eight hundred fifty, or at least nine hundred chromatin regions selected from the list of chromatin regions in  FIG. 9A  and  FIG. 9B .   
     
     
         15 . The solid support of  claim 14 , wherein each unique oligonucleotide probe is complementary to at least a portion of a chromatin region selected from the list of chromatin regions in  FIG. 9A  of  FIG. 9B  or a complement thereof 
     
     
         16 . A kit or system comprising the solid support of  claim 14 . 
     
     
         17 . The kit or system of  claim 16 , further comprising a reagent for detection of HNF1b, wherein the reagent is an antibody or fragment thereof that specifically binds to HNF1b. 
     
     
         18 . A method for forming a plurality of duplexed molecules, the method comprising:
 contacting labeled nucleic acid fragments to the set of oligonucleotides probes bound to the solid support of  claim 14  under conditions sufficient to form a plurality of duplexed molecules, wherein each duplexed molecule comprises (i) a tagged DNA fragment or derivative thereof representing an accessible chromatin region (ACR) of a morphologically intact nuclei and (ii) an oligonucleotide probe bound to the solid support.   
     
     
         19 . A method for treating pancreatic ductal adenocarcinoma in a patient in need thereof, the method comprising:
 resecting cancerous tissue, wherein prior to said resection, a biological sample from the patient has been tested to determine chromatin accessibility of a first group of differentially accessible chromatin regions and, optionally, a second group of differentially accessible chromatin regions, wherein accessibility of said first group of differentially accessible chromatin regions is associated with a good prognosis and accessibility of said second group of differentially accessible chromatin regions is associated with a poor prognosis; or   administering neo-adjuvant chemotherapy followed by surgical resection of cancerous tissue, wherein prior to administering the neo-adjuvant chemotherapy, a biological sample from the patient has been tested to determine chromatin accessibility of a first group of differentially accessible chromatin regions and, optionally, a second group of differentially accessible chromatin regions, wherein accessibility of said first group of differentially accessible chromatin regions is associated with a good prognosis and accessibility of said second group of differentially accessible chromatin regions is associated with a poor prognosis; or   administering chemotherapy alone, wherein prior to administering the chemotherapy alone, a biological sample from the patient has been tested to determine chromatin accessibility of a first group of differentially accessible chromatin regions and, optionally, a second group of differentially accessible chromatin regions, wherein accessibility of said first group of differentially accessible chromatin regions is associated with a good prognosis and accessibility of said second group of differentially accessible chromatin regions is associated with a poor prognosis; or   administering an immunotherapy agent to the patient, wherein prior to administering the immunotherapy agent, a biological sample from the patient has been tested to determine chromatin accessibility of a first group of differentially accessible chromatin regions and, optionally, a second group of differentially accessible chromatin regions, wherein accessibility of said first group of differentially accessible chromatin regions is associated with a good prognosis and accessibility of said second group of differentially accessible chromatin regions is associated with a poor prognosis;   administering a kinase inhibitor to the patient, wherein prior to administering the kinase inhibitor, a biological sample from the patient has been tested to determine chromatin accessibility of a first group of differentially accessible chromatin regions and, optionally, a second group of differentially accessible chromatin regions, wherein accessibility of said first group of differentially accessible chromatin regions is associated with a good prognosis and accessibility of said second group of differentially accessible chromatin regions is associated with a poor prognosis; or   administering an epigenetic drug to the patient, wherein prior to administering the epigenetic drug, a biological sample from the patient has been tested to determine chromatin accessibility of a first group of differentially accessible chromatin regions and, optionally, a second group of differentially accessible chromatin regions, wherein accessibility of said first group of differentially accessible chromatin regions is associated with a good prognosis and accessibility of said second group of differentially accessible chromatin regions is associated with a poor prognosis.   
     
     
         20 . The method of  claim 19 , wherein said first group of differentially accessible chromatin regions comprises one or more, preferably two or more, or more preferably fifty or more, chromatin regions selected from  FIG. 9A  and/or said second group of differentially accessible chromatin regions comprises one or more, preferably two or more, or more preferably fifty or more, chromatin regions selected from  FIG. 9B .