Oncogenic ALL-1 Fusion Proteins for Targeting Drosha-Mediated MicroRNA Processing
AssigneeThe Ohio State University Research Foundation
InventorCarlo M. Croce
Life of this patent
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Abstract
Disclosed are compositions and methods for reducing the proliferation of ALL cancer cells through targeted interactions with ALL1 fusion proteins.
Claims32
An oligomeric compound targeted to a Drosha recognition region within the pri-miRNA transcript from which at least one miR in Table 1 is derived.
An oligomeric compound targeted to a Drosha recognition region within the pri-miRNA transcript from which at least one miR in miR-191 is derived.
The oligomeric compound of any of the preceding claims, wherein the oligomeric compound is an antisense oligonucleotide.
The oligomeric compound of any of the preceding claims, wherein the Drosha recognition region is that of miR-191.
The oligomeric compound of any of the preceding claims, wherein the oligomeric compound is capable of altering the levels of pri-miR-191.
A method of modulating pri-miR-191 levels in a cell comprising contacting the cell with the oligomeric compound of any of the preceding claims.
The method of any of the preceding claims, wherein the modulation results in the alteration of pri-miR-191 levels.
An oligomeric compound that targets a region flanking or overlapping a Drosha recognition region within a pri-miRNA.
An oligomeric compound that targets a region flanking or overlapping a Drosha cleavage site.
An oligomeric compound that increases levels of a pri-miRNA, comprising an oligomeric compound about 15 to about 30 nucleobases in length targeted to a Drosha recognition region within a polycistronic pri-miRNA transcript, wherein the polycistronic pri-miRNA transcript can be that from which the miRNAs listed in Table 1 are derived.
The compound as in any of the preceding claims, wherein the Drosha recognition region can be one or more of the miRNAs listed in Table 1.
The oligomeric compound of any of the preceding claims, wherein the compound may be antisense oligonucleotides, and may contain one or more chemical modifications.
A method of modulating the levels of small non-coding RNAs, particularly pri-miRNAs, in cells, tissues or animals comprising contacting the cells, tissues or animals with one or more of the compounds or compositions of the invention.
A method of modulating the levels of miRs derived from a polycistronic pri-miR transcript in a cell comprising selecting a polycistronic pri-miR transcript, selecting a Drosha recognition region of a single miRNA derived from the selected polycistronic pri-miR transcript, selecting an oligomeric compound 15 to 30 nucleotides in length targeted to or sufficiently complementary to the selected Drosha recognition region, and contacting the cell with the oligomeric compound.
A method of any of the preceding claims, including modulating the levels of a single mature miRNA derived from the selected polycistronic pri-miRNA, or alternatively modulating the levels of two or more mature miRNAs derived from the selected polycistronic pri-miRNA.
A method of modulating the levels of pri-miRNAs from those listed in Table 1 comprising contacting a cell with an oligomeric compound targeted to or sufficiently complementary to Drosha-recognition regions on such pri-miRNAs.
A method for selectively modulating a single member of a miR family in a cell comprising selecting a member of a miR family derived from a pri-miR transcript, identifying one or more oligomeric compounds targeted to or sufficiently complementary to the Drosha recognition region of a the selected pri-miR transcript, wherein the identified oligomeric compounds lack sufficient complementarity to the Drosha recognition regions of pri-miR transcripts from which other members of the miR family are derived, and contacting the cell with such an identified oligomeric compound.
An oligomeric compound comprising a first strand and a second strand wherein at least one strand contains a modification and wherein a portion of one of the oligomeric compound strands is capable of hybridizing to a small non-coding RNA target nucleic acid.
An oligomeric compound comprising a first region and a second region and optionally a third region wherein at least one region contains a modification and wherein a portion of the oligomeric compound is capable of hybridizing to a small non-coding RNA target nucleic acid.
A method for identifying oligomeric compounds capable of modulating pri-miRNA levels wherein a pri-miRNA is selected, and oligomeric compounds are designed such that they are targeted to or sufficiently complementary to various target segments within a pri-miRNA sequence, including oligomeric compounds targeted to and overlapping the mature miRNA sequence within the pri-miRNA.
A method of the preceding claim, wherein an increase in the level of a pri-miRNA in cells contacted with the oligomeric compounds as compared to cells not contacted with the oligomeric compounds indicates that the oligomeric compound modulates the pri-miRNA level.
A method for identifying small molecules capable of modulating pri-miRNA levels wherein a pri-miRNA is selected, and small molecules are evaluated for their ability of modulate pri-miRNA levels, and wherein the small molecules may bind to the regions of the pri-miR containing or overlapping the mature miRNA sequence, or the Drosha recognition region.
The method of the preceding claim, wherein an increase in the level of a pri-miRNA in cells contacted with the small molecules as compared to cells not contacted with the small molecules indicates that the small molecule modulates the pri-miRNA levels.
A method of diagnosing whether a subject has, or is at risk for developing, acute lymphomic leukemia (ALL), comprising:
- measuring the level of one or more miR gene products selected from the list in Table 1 in a test sample from the subject,
- wherein an alteration in the level of the miR gene product in the test sample, relative to the level of a corresponding miR gene product in a control sample, is indicative of the subject either having, or being at risk for developing, ALL.
The method of any of the preceding claims, wherein the level of the at least one miR gene product in the test sample is less than the level of the corresponding miR gene product in the control sample.
The method of any of the preceding claims, wherein the level of the at least one miR gene product in the test sample is greater than the level of the corresponding miR gene product in the control sample.
A method of determining the prognosis of a subject with ALL cancer, comprising:
- measuring the level of one or more miR gene product listed in Table 1 in a test sample from the subject,
- wherein the miR gene product is associated with an adverse prognosis in ALL;
- and
- wherein an alteration in the level of the at least one miR gene product in the test sample, relative to the level of a corresponding miR gene product in a control sample, is indicative of an adverse prognosis.
A method of diagnosing whether a subject has, or is at risk for developing, ALL, comprising:
- (1) reverse transcribing RNA from a test sample obtained from the subject to provide a set of target oligodeoxynucleotides;
- (2) hybridizing the target oligodeoxynucleotides to a microarray comprising miRNA-specific probe oligonucleotides to provide a hybridization profile for the test sample;
- and
- (3) comparing the test sample hybridization profile to a hybridization profile generated from a control sample,
- wherein an alteration in the signal of at least one miRNA is indicative of the subject either having, or being at risk for developing, ALL.
The method of any of the preceding claims, wherein the signal of at least one miRNA, relative to the signal generated from the control sample, is down-regulated.
The method of any of the preceding claims, wherein the signal of at least one miRNA, relative to the signal generated from the control sample, is up-regulated.
A method of diagnosing whether a subject has, or is at risk for developing, ALL with an adverse prognosis in a subject, comprising:
- (1) reverse transcribing RNA from a test sample obtained from the subject to provide a set of target oligodeoxynucleotides;
- (2) hybridizing the target oligodeoxynucleotides to a microarray comprising miRNA-specific probe oligonucleotides to provide a hybridization profile for the test sample;
- and
- (3) comparing the test sample hybridization profile to a hybridization profile generated from a control sample,
- wherein an alteration in the signal is indicative of the subject either having, or being at risk for developing, ALL with an adverse prognosis.
A method of treating ALL in a subject who has ALL in which at least one miR gene product is down-regulated or up-regulated in the cancer cells of the subject relative to control cells, comprising:
- (1) when the at least one miR gene product is down-regulated in the cancer cells, administering to the subject an effective amount of at least one isolated miR gene product, or an isolated variant or biologically-active fragment thereof, such that proliferation of cancer cells in the subject is inhibited;
- or
- (2) when the at least one miR gene product is up-regulated in the cancer cells, administering to the subject an effective amount of at least one compound for inhibiting expression of the at least one miR gene product, such that proliferation of cancer cells in the subject is inhibited.
Dependencies are inferred from the claim text.