Compositions and methods for modulating hepatocyte nuclear factor 4-alpha (HNF4α) gene expression
The present invention provides agents and compositions for modulating expression (e.g., enhanced or reduced expression) of a hepatocyte nuclear factor 4 alpha (HNF4α) gene by targeting an HNF4α expression control region and methods of use thereof for treating an HNF4α associated disorder, e.g., cirrhosis.
1. A site-specific hepatocyte nuclear factor 4a (HNF4α) disrupting agent, comprising a site-specific HNF4α targeting moiety which targets an HNF4α expression control region, and wherein the HNF4α targeting moiety comprises a DNA-binding domain of a zinc finger (ZNF) polypeptide, or fragment thereof, that specifically binds to the HNF4α expression control region, wherein the DNA-binding domain of the ZNF polypeptide comprises an amino acid sequence having at least 85% amino acid identity to the entire amino acid sequence of any one of the amino acid sequences selected from the group consisting of SEQ ID NOs: 103, 107, 111, 115, 119, 123, 127, 131, 135, 139, 143, 147, 151, 155, and 159.
2. The site-specific HNF4α disrupting agent of claim 1 , wherein the site-specific HNF4α disrupting agent is present in a composition.
3. A method of modulating expression of hepatocyte nuclear factor 4 alpha (HNF4α) in a cell, the method comprising contacting the cell with a site-specific HNF4α disrupting agent of claim 1 , thereby modulating expression of HNF4α in the cell.
4. The method of claim 3 , wherein the cell is within a subject, wherein the subject has an HNF4α-associated disease.
5. The method of claim 4 , wherein the HNF4α-associated disease is selected from the group consisting of fatty liver (steatosis), nonalcoholic steatohepatitis (NASH), cirrhosis of the liver, accumulation of fat in the liver, inflammation of the liver, hepatocellular necrosis, liver fibrosis, and nonalcoholic fatty liver disease (NAFLD), polycystic kidney disease, inflammatory bowel disease (IBD), and MODY I.
6. A method for treating a subject having an HNF4α-associated disease, comprising administering to the subject a therapeutically effective amount of the site-specific HNF4α disrupting agent of claim 1 , thereby treating the subject.
7. The method of claim 6 , wherein the HNF4α-associated disease is selected from the group consisting of fatty liver (steatosis), nonalcoholic steatohepatitis (NASH), cirrhosis of the liver, accumulation of fat in the liver, inflammation of the liver, hepatocellular necrosis, liver fibrosis, and nonalcoholic fatty liver disease (NAFLD) and the site-specific HNF4α disrupting agent enhances expression of HNF4α in the subject.
8. The site-specific HNF4α disrupting agent of claim 1 , wherein the HNF4α expression control region comprises the nucleotide sequence of SEQ ID NO:118.
9. The site-specific HNF4α disrupting agent of claim 1 , wherein the HNF4α expression control region comprises the nucleotide sequence of SEQ ID NO:126.
10. The site-specific HNF4α disrupting agent of claim 1 , wherein the DNA-binding domain of the ZNF polypeptide comprises an amino acid sequence having at least 85% amino acid identity to the amino acid sequence of SEQ ID NO: 119.
11. The site-specific HNF4α disrupting agent of claim 1 , wherein the DNA-binding domain of the ZNF polypeptide comprises an amino acid sequence having at least 85% amino acid identity to the amino acid sequence of SEQ ID NO: 127.
12. The site-specific HNF4α disrupting agent of claim 1 , wherein the agent further comprises an effector molecule, and wherein the effector molecule is fused to the DNA-binding domain of the ZNF polypeptide.
13. The site-specific HNF4α disrupting agent of claim 12 , wherein the effector molecule is selected from the group consisting of a physical blocker, an epigenetic recruiter, and an epigenetic CpG modifier.
14. The site-specific HNF4α disrupting agent of claim 13 , wherein the epigenetic recruiter is selected from the group consisting of a transcriptional enhancer and a transcriptional repressor.
15. The site-specific HNF4α disrupting agent of claim 13 , wherein the CpG modifier is selected from the group consisting of a DNA methylase, a DNA demethylase, a histone modifying agent, and a histone deacetylase.
16. The site-specific HNF4α disrupting agent of claim 12 , wherein the effector molecule is VPR (VP64-p65-Rta).
17. The site-specific HNF4α disrupting agent of claim 16 , wherein the VPR comprises an amino acid sequence having at least 85% amino acid identity to the amino acid sequence of SEQ ID NO: 66, and wherein the DNA-binding domain of the ZNF polypeptide comprises an amino acid sequence having at least 85% amino acid identity to the amino acid sequence of SEQ ID NO: 119.
18. The site-specific HNF4α disrupting agent of claim 12 , wherein the effector molecule is P300.
19. The site-specific HNF4α disrupting agent of claim 18 , wherein the P300 comprises an amino acid sequence having at least 85% amino acid identity to the amino acid sequence of SEQ ID NO: 67, and wherein the DNA-binding domain of the ZNF polypeptide comprises an amino acid sequence having at least 85% amino acid identity to the amino acid sequence of SEQ ID NO: 127.
20. The site-specific HNF4α disrupting agent of claim 1 , wherein the DNA-binding domain of the ZNF polypeptide comprises an amino acid sequence having at least 90% amino acid identity to the entire amino acid sequence of any one of the amino acid sequences selected from the group consisting of SEQ ID NOs: 103, 107, 111, 115, 119, 123, 127, 131, 135, 139, 143, 147, 151, 155, and 159.
21. The site-specific HNF4α disrupting agent of claim 1 , wherein the DNA-binding domain of the ZNF polypeptide comprises an amino acid sequence having at least 95% amino acid identity to the entire amino acid sequence of any one of the amino acid sequences selected from the group consisting of SEQ ID NOs: 103, 107, 111, 115, 119, 123, 127, 131, 135, 139, 143, 147, 151, 155, and 159.
22. The site-specific HNF4α disrupting agent of claim 20 , wherein the DNA-binding domain of the ZNF polypeptide comprises an amino acid sequence having at least 90% amino acid identity to the amino acid sequence of SEQ ID NO: 119.
23. The site-specific HNF4α disrupting agent of claim 21 , wherein the DNA-binding domain of the ZNF polypeptide comprises an amino acid sequence having at least 95% amino acid identity to the amino acid sequence of SEQ ID NO: 119.
24. The site-specific HNF4α disrupting agent of claim 1 , wherein the DNA-binding domain of the ZNF polypeptide comprises the amino acid sequence of SEQ ID NO: 119.
25. The site-specific HNF4α disrupting agent of claim 20 , wherein the DNA-binding domain of the ZNF polypeptide comprises an amino acid sequence having at least 90% amino acid identity to the amino acid sequence of SEQ ID NO: 127.
26. The site-specific HNF4α disrupting agent of claim 21 , wherein the DNA-binding domain of the ZNF polypeptide comprises an amino acid sequence having at least 95% amino acid identity to the amino acid sequence of SEQ ID NO: 127.
27. The site-specific HNF4α disrupting agent of claim 1 , wherein the DNA-binding domain of the ZNF polypeptide comprises the amino acid sequence of SEQ ID NO: 127.
28. The site-specific HNF4α disrupting agent of claim 16 , wherein the VPR comprises the amino acid sequence of SEQ ID NO: 66.
29. The site-specific HNF4α disrupting agent of claim 16 , wherein the VPR comprises an amino acid sequence having at least 90% amino acid identity to the amino acid sequence of SEQ ID NO: 66, and wherein the DNA-binding domain of the ZNF polypeptide comprises an amino acid sequence having at least 90% amino acid identity to the amino acid sequence of SEQ ID NO: 119.
30. The site-specific HNF4α disrupting agent of claim 16 , wherein the VPR comprises an amino acid sequence having at least 95% amino acid identity to the amino acid sequence of SEQ ID NO: 66, and wherein the DNA-binding domain of the ZNF polypeptide comprises an amino acid sequence having at least 95% amino acid identity to the amino acid sequence of SEQ ID NO: 119.
31. The site-specific HNF4α disrupting agent of claim 16 , wherein the VPR comprises the amino acid sequence of SEQ ID NO: 66, and wherein the DNA-binding domain of the ZNF polypeptide comprises the amino acid sequence of SEQ ID NO: 119.
32. The site-specific HNF4α disrupting agent of claim 18 , wherein the P300 comprises the amino acid sequence of SEQ ID NO: 67.
33. The site-specific HNF4α disrupting agent of claim 18 , wherein the P300 comprises an amino acid sequence having at least 90% amino acid identity to the amino acid sequence of SEQ ID NO: 67, and wherein the DNA-binding domain of the ZNF polypeptide comprises an amino acid sequence having at least 90% amino acid identity to the amino acid sequence of SEQ ID NO: 127.
34. The site-specific HNF4α disrupting agent of claim 18 , wherein the P300 comprises an amino acid sequence having at least 95% amino acid identity to the amino acid sequence of SEQ ID NO: 67, and wherein the DNA-binding domain of the ZNF polypeptide comprises an amino acid sequence having at least 95% amino acid identity to the amino acid sequence of SEQ ID NO: 127.
35. The site-specific HNF4α disrupting agent of claim 18 , wherein the P300 comprises the amino acid sequence of SEQ ID NO: 67, and wherein the DNA-binding domain of the ZNF polypeptide comprises the amino acid sequence of SEQ ID NO: 127.
36. The site-specific HNF4α disrupting agent of claim 16 , wherein the site-specific HNF4α disrupting agent comprises an amino acid sequence having at least 90% amino acid identity to the entire amino acid sequence of SEQ ID NO:116.
37. The site-specific HNF4α disrupting agent of claim 16 , wherein the site-specific HNF4α disrupting agent comprises an amino acid sequence having at least 95% amino acid identity to the entire amino acid sequence of SEQ ID NO:116.