Recombinant promoters and vectors for protein expression in liver and use thereof

1. A recombinant nucleic acid molecule, comprising:

a liver-specific promoter comprising a first response element of no more than 160 nucleotides in length that comprises:

a HNF1a transcription factor (TF) binding site;

a HNF1-1 TF binding site;

a HNF4 TF binding site;

a HNF3a TF binding site;

a HNF1-2 TF binding site;

a HNF3-2 TF binding site;

a HP1 TF binding site

a TATA box; and

a Transcription Start Site.

2. The recombinant nucleic acid molecule of claim 1 , wherein:

the HNF1a TF binding site comprises or consists of nucleotides 1-12 of SEQ ID NO: 4;

the HNF1-1 TF binding site comprises or consists of nucleotides 16-23 of SEQ ID NO: 4;

the HNF4 TF binding site comprises or consists of nucleotides 26-36 of SEQ ID NO: 4;

the HNF3a TF binding site comprises or consists of nucleotides 39-45 of SEQ ID NO: 4;

the HNF1-2 TF binding site comprises or consists of nucleotides 48-62 of SEQ ID NO: 4;

the HNF3-2 TF binding site comprises or consists of nucleotides 65-71 of SEQ ID NO: 4;

the HP1 TF binding site comprises or consists of nucleotides 75-87 of SEQ ID NO: 4;

the TATA box comprises or consists of nucleotides 108-114 of SEQ ID NO: 4; and

the Transcription Start Site (TSS) comprises or consists of nucleotides 116-146 of SEQ ID NO: 4.

3. The recombinant nucleic acid molecule of claim 1 , wherein the first response element comprises, from 5′ to 3′, the HNF1a TF binding site, the HNF1-1 TF binding site, the HNF4 TF binding site, the HNF3a TF binding site, the HNF1-2 TF binding site, the HNF3-2 TF binding site, the HP1 TF binding site, the TATA box, and the Transcription Start Site (TSS).

4. The recombinant nucleic acid molecule of claim 1 , wherein the first response element is no more than 150 nucleotides in length.

5. The recombinant nucleic acid molecule of claim 1 , wherein the first response element is 146 nucleotides in length.

6. The recombinant nucleic acid molecule of claim 1 , wherein the first response element comprises or consists of a nucleotide sequence at least 90% identical to SEQ ID NO: 4.

7. The recombinant nucleic acid molecule of claim 6 , wherein the first response element comprises or consists of the nucleotide sequence set forth as SEQ ID NO: 4.

8. The recombinant nucleic acid molecule of claim 1 , wherein the promoter consists of the first response element.

9. The recombinant nucleic acid molecule of claim 1 , further comprising a second response element upstream of the first response element, the second response element comprising one of:

a HSh response element comprising or consisting of a nucleotide sequence at least 90% identical to SEQ ID NO: 111;

a 5′HS response element comprising or consisting of a nucleotide sequence at least 90% identical to nucleotides 6-32 of SEQ ID NO: 111; or

a 3′HS response element comprising or consisting of a nucleotide sequence at least 90% identical to nucleotides 44-68 of SEQ ID NO: 111.

10. The recombinant nucleic acid molecule of claim 9 , wherein the

the HSh response element comprises or consists of the nucleotide sequence set forth as SEQ ID NO: 111;

the 5′HS response element comprises or consists of nucleotides 6-32 of SEQ ID NO: 111; or

the 3′HS response element comprises or consists of nucleotides 44-68 of SEQ ID NO: 111.

11. The recombinant nucleic acid molecule of claim 10 , wherein the

the HSh response element consists of the nucleotide sequence set forth as SEQ ID NO: 111;

the 5′HS response element consists of nucleotides 6-32 of SEQ ID NO: 111; or

the 3′HS response element consists of nucleotides 44-68 of SEQ ID NO: 111.

12. The recombinant nucleic acid molecule of claim 9 , wherein the recombinant promoter comprises or consists of a nucleotide sequence at least 90% identical to one of SEQ ID NO: 102 (HSh-HCB), SEQ ID NO: 104 (5′HSh-HCB), or SEQ ID NO: 103 (3′HSh-HCB).

13. The recombinant nucleic acid molecule of claim 12 , wherein the recombinant promoter comprises or consists of the nucleotide sequence set forth as SEQ ID NO: 102 (HSh-HCB), SEQ ID NO: 104 (5′HSh-HCB), or SEQ ID NO: 103 (3′HSh-HCB).

14. A recombinant nucleic acid molecule comprising or consisting of the nucleotide sequence set forth as any one of SEQ ID NO: 5 (shortABP-HP1-God-TSS), SEQ ID NO: 7 (ABP-HP1-God-TSS), SEQ ID NO: 105 (HSh-SynO-TSS), SEQ ID NO: 106 (sHS-SynO-TSS), SEQ ID NO: 107 (Agro), SEQ ID NO: 108 (HS-SynO-TSS), or SEQ ID NO: 112 (HNF1-ShortABPExact-SynO-TSS-Int), or a nucleotide sequence at least 90% identical thereto.

15. A vector comprising the recombinant nucleic acid molecule of claim 1 .

16. The vector of claim 15 , wherein the vector is a viral vector.

17. The vector of claim 16 , wherein the viral vector is an AAV vector.

18. The vector of claim 15 , wherein the viral vector is a gamma-retroviral vector, a lentiviral vector, or an adenoviral vector.

19. The vector of claim 15 , comprising a nucleic acid molecule encoding a clotting factor that is operably linked to the promoter.

20. The vector of claim 19 , wherein the clotting factor is fVIII, or an ET3 or B domain deleted human (HSQ) fVIII variant.

21. The vector of claim 20 , wherein the fVIII comprises the nucleic acid sequence set forth as SEQ ID NO: 2, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 125, or SEQ ID NO: 126, or a nucleic acid sequence at least 90% identical to SEQ ID NO: 2, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 125, or SEQ ID NO: 126.

22. The vector of claim 19 , wherein the clotting factor is fIX.

23. The vector of claim 22 , wherein the fIX comprises the nucleic acid sequence set forth as SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 124, or SEQ ID NO: 127, or a nucleic acid sequence at least 90% identical SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 124, or SEQ ID NO: 127.

24. A composition comprising the vector of claim 15 in a pharmaceutically acceptable carrier.

25. An isolated nucleic acid molecule, comprising:

a nucleic acid sequence encoding fVIII and comprising the nucleotide sequence set forth as one of SEQ ID NO: 2, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 125, or SEQ ID NO: 126, or a nucleotide sequence at least 90% identical to one of SEQ ID NO: 2, SEQ ID NO: 11, SEQ ID NO: 12 SEQ ID NO: 125, or SEQ ID NO: 126; or

a nucleic acid sequence encoding fIX and comprising the nucleotide sequence set forth as one of SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 124, or SEQ ID NO: 127, or a nucleotide sequence at least 90% identical to one of SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 124, or SEQ ID NO: 127.

26. A method of inducing blood clotting in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of the vector of claim 19 .

27. A method of treating a subject with a clotting disorder, comprising selecting a subject with the clotting disorder and administering to the subject a therapeutically effective amount of the vector of claim 19 .

28. The method of claim 27 , wherein the clotting disorder is:

hemophilia A and the subject is administered a vector comprising a nucleic acid molecule encoding a protein with fVIII activity; or

hemophilia B and the subject is administered a vector comprising a nucleic acid molecule encoding a protein with fIX activity.