Nucleic acid encoding a retinoblastoma binding protein (RBP-7) and polymorphic markers associated with said nucleic acid

• US 20030170647A1
• Filed: 04/20/2002
• Published: 09/11/2003
• Est. Priority Date: 06/30/1998
• Status: Abandoned Application

• Current Assignee: Serono Genetics Institute S.A. (Merck & Co., Inc.)
• Original Assignee: Genset SA (Merck & Co., Inc.)
• Inventors: Bougueleret, Lydie
• Application Number:
  US10/126,704
• Publication Number:
  US 20030170647A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: A01K 2217/05 Animals comprising random inserted nucleic acids (transgenic)
• CPC Class Codes: A01K 2217/075 inducing loss of function, i.e. knock out
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C07K 14/47 from mammals
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/172 Haplotypes

Abstract

The present invention is directed to a polynucleotide comprising open reading frames defining a coding region encoding a retinoblastoma binding protein (RBP-7) as well as regulatory regions located both at the 5′en d and the 3′ end of said coding region. The present invention also pertains to a polynucleotide carrying the natural regulation signals of the RBP-7 gene which is useful in order to express a heterologous nucleic acid in host cells or host organisms as well as functionally active regulatory polynucleotides derived from said regulatory region. The invention also concerns polypeptides encoded by the coding region of the RBP-7 gene. The invention also deals with antibodies directed specifically against such polypeptides that are useful as diagnostic reagents. The invention also comprises genetic markers, namely biallelic markers, that are means that may be useful for the diagnosis of diseases related to an alteration in the regulation or in the coding regions of the RBP-7 gene and for the prognosis/diagnosis of an eventual treatment with therapeutic agents, especially agents acting on pathologies involving abnormal cell proliferation and/or abnormal cell differentiation

Claims

1. A purified or isolated polynucleotide comprising a contiguous span of at least 12 nucleotides of SEQ ID No. 1 or the complements thereof, wherein said contiguous span comprises at least 1 of the following nucleotide positions of SEQ ID No. 1:

1-481, 666-1465, 1521-67592, 67704-71118, 71185-72598, 72690-75543, 75624-81841, 81934-83019, 83406-87901, 88041-93856, 93937-97158, 97236-98962, 99086-103188, 103745-104303, 104654-105084, 105180-106682, 106781-107798, 107897-108392, 108552-114335, 114418-114491, 114594-132246, 132332-134150, 134350-145565, 145842-146332, 146775-150446, 150542-152959, 153176-155590, 155738-159701, 160466-161028, and 161453-162450

2. A purified or isolated polynucleotide comprising a contiguous span of at least 12 nucleotides of SEQ ID No. 4 or the complements thereof, wherein said contiguous span comprises at least I of the following nucleotide positions of SEQ D No. 4:

1-208, 1307-1350, 1703-1865, 2107-2180, 2843-3333, 3871-3882, 4222-4276, and 5017-5579.

3. A purified or isolated nucleic acid comprising a nucleotide sequence selected >

from the group of SEQ ID Nos. 5-28, a sequence complementary thereto or a fragment or a variant thereof.

4. A purified or isolated nucleic acid comprising a combination of at least two polynucleotides selected from the group consisting of SEQ ID Nos. 5-28, wherein the polynucleotides are arranged within the nucleic acid, from the 5′

end to the 3′

end of said nucleic acid, in the same order than in SEQ ID No 1

5. An oligonucleotide of at least 8 nucleotides in length that hybridizes under stringent hybridization conditions with a nucleic acid selected from the group consisting of the nucleotide sequences 1-481, 666-1465, 1521-67592, 67704-71118, 71185-72598, 72690-75543, 75624-81841, 81934-83019, 83406-87901, 88041-93856, 93937-97158, 97236-98962, 99086-103188, 103745-104303, 104654-105084, 105180-106682, 106781-107798, 107897-108392, 108552-114335, 114418-114491, 114594-132246, 132332-134150, 134350-145565, 145842-146332, 146775-150446, 150542-152959, 153176-155590, 155738-159701, 160466-161028, and 161453-162450 of SEQ ID No 1 or a sequence complementary thereto

6. An oligonucleotide of at least 8 nucleotides in length that hybridizes under stringent hybridization conditions with a nucleic acid selected from the group consisting of the nucleotide sequences 1-208, 1307-1350, 1703-1865, 2107-2180, 2843-3333, 3871-3882, 4222-4276, and 5017-5579 of SEQ ID No. 4 or a sequence complementary thereto

7. An isolated, purified, or recombinant polynucleotide consisting essentially of a contiguous span of 8 to 50 nucleotides of any one of SEQ ID Nos. 1 and 4 and the complement thereof, wherein said span includes a biallelic marker of RBP-7.

8. A polynucleotide according to claim 7, wherein said biallelic marker of RBP-7 is selected from the group consisting of A1 to A21, and the complements thereof

9. A polynucleotide according to claim 7, wherein said contiguous span is 18 to 47 nucleotides in length and said biallelic marker is within 4 nucleotides of the center of said polynucleotide.

10. A polynucleotide according to claim 9, wherein said polynucleotide consists of said contiguous span and said contiguous span is 25 nucleotides in length and said biallelic marker is at the center of said polynucleotide.

11. A polynucleotide according to claim 9, wherein said polynucleotide consists essentially of a sequence selected from the sequences SEQ ID Nos. 30-71 and the complementary sequences thereto.

12. A polynucleotide according to claim 7, wherein the 3′

end of said contiguous span is located at the 3′

end of said polynucleotide and said biallelic marker is present at the 3′

end of said polynucleotide.

13. An isolated, purified, or recombinant polynucleotide consisting essentially of a contiguous span of 8 to 50 nucleotides of any one of SEQ ID Nos 1 and 4 and the complement thereof, wherein the 3′

end of said contiguous span is located at the 3′

end of said polynucleotide, and wherein the 3′

end of said polynucleotide is located within 20 nucleotides upstream of a biallelic marker of RBP-7 in said sequence

14. A polynucleotide according to claim 13, wherein the 3′

end of said polynucleotide is located 1 nucleotide upstream of said biallelic marker of RBP-7 in said sequence.

15. A polynucleotide according to claim 14, wherein said polynucleotide consists essentially of a sequence selected from the sequences of SEQ ID Nos 102-136.

16. An isolated, purified, or recombinant polynucleotide consisting essentially of a sequence selected from the sequences of SEQ ID Nos. 72-101

17. An isolated, purified, or recombinant polynucleotide which encodes a polypeptide comprising a contiguous span of at least 6 amino acids of SEQ ID No. 29.

18. An isolated, purified, or recombinant polynucleotide for use in hybridization assays, sequencing assays, and enzyme-based mismatch detection assays for determining the identity of the nucleotide at a biallelic marker of RBP-7.

19. A solid support having a polynucleotide attached thereto, wherein said polynucleotide is selected from the group consisting of

a) a polynucleotide comprising a contiguous span of at least 12 nucleotides of SEQ ID No. 1 or the complements thereof, wherein said contiguous span comprises at least 1 of the following nucleotide positions of SEQ ID No 1:

1-481, 666-1465, 1521-67592, 67704-71118, 71185-72598, 72690-75543, 75624-81841, 81934-83019, 83406-87901, 88041-93856, 93937-97158, 97236-98962, 99086-103188, 103745-104303, 104654-105084, 105180-106682, 106781-107798, 107897-108392, 108552-114335, 114418-114491, 114594-132246, 132332-134150, 134350-145565, 145842-146332, 146775-150446, 150542-152959, 153176-155590, 155738-159701, 160466-161028, and 161453-162450;

b) a polynucleotides comprising a contiguous span of at least 12 nucleotides of SEQ ID No 4 or the complements thereof, wherein said contiguous span comprises at least 1 of the following nucleotide positions of SEQ ID No. 4;

1-208, 1307-1350, 1703-1865, 2107-2180, 2843-3333, 3871-3882, 4222-4276, and 5017-5579;

c) a polynucleotide consisting essentially of a contiguous span of 8 to 50 nucleotides of any one of SEQ ID Nos. 1 and 4 and the complement thereof, wherein said span includes a biallelic marker of RBP-7,

d) a polynucleotide consisting essentially of a contiguous span of 8 to 50 nucleotides of any one of SEQ ID Nos. 1 and 4 and the complement thereof, wherein the 3′

end of said contiguous span is located at the 3′

end of said polynucleotide, and wherein the 3′

end of said polynucleotide is located within 20 nucleotides upstream of a biallelic marker of RBP-7 in said sequence;

e) a polynucleotide consisting essentially of a sequence selected from the sequences of SEQ ID Nos. 72-101,

f) a polynucleotide which encodes a polypeptide comprising a contiguous span of at least 6 amino acids of SEQ ID No 29; and

g) a polynucleotide for use in hybridization assays, sequencing assays, and enzyme-based mismatch detection assays for determining the identity of the nucleotide at a biallelic marker of RBP-7

20. An array of polynucleotides comprising at least one polynucleotide according to claim 19

21. An array according to claim 20, wherein said array is addressable.

22. A polynucleotide having a label thereon, wherein said polynucleotide is selected from the group consisting of.

a) a polynucleotide comprising a contiguous span of at least 12 nucleotides of SEQ ID No 1 or the complements thereof, wherein said contiguous span comprises at least 1 of the following nucleotide positions of SEQ ID No 1:

1-481, 666-1465, 1521-67592, 67704-71118, 71185-72598, 72690-75543, 75624-81841, 81934-83019, 83406-87901, 88041-93856, 93937-97158, 97236-98962, 99086-103188, 103745-104303, 104654-105084, 105180-106682, 106781-107798, 107897-108392, 108552-114335, 114418-114491, 114594-132246, 132332-134150, 134350-145565, 145842-146332, 146775-150446, 150542-152959, 153176-155590, 155738-159701, 160466-161028, and 161453-162450;

b) a polynucleotides comprising a contiguous span of at least 12 nucleotides of SEQ ID No 4 or the complements thereof, wherein said contiguous span comprises at least 1 of the following nucleotide positions of SEQ ID No. 4;

1-208, 1307-1350, 1703-1865, 2107-2180, 2843-3333, 3871-3882, 4222-4276, and 5017-5579;

c) a polynucleotide consisting essentially of a contiguous span of 8 to 50 nucleotides of any one of SEQ ID Nos 1 and 4 and the complement thereof, wherein said span includes a biallelic marker of RBP-7,

d) a polynucleotide consisting essentially of a contiguous span of 8 to 50 nucleotides of any one of SEQ ID Nos. 1 and 4 and the complement thereof, wherein the 3′

end of said contiguous span is located at the 3′

end of said polynucleotide, and wherein the 3′

end of said polynucleotide is located within 20 nucleotides upstream of a biallelic marker of RBP-7 in said sequence;

e) a polynucleotide consisting essentially of a sequence selected from the sequences of SEQ ID Nos. 72-101;

f) a polynucleotide which encodes a polypeptide comprising a contiguous span of at least 6 amino acids of SEQ ID No. 29; and

g) a polynucleotide for use in hybridization assays, sequencing assays, and enzyme-based mismatch detection assays for determining the identity of the nucleotide at a biallelic marker of RBP-7

23. A recombinant vector comprising a polynucleotide selected from the group consisting of:

a) a polynucleotide comprising a contiguous span of at least 12 nucleotides of SEQ ID No. 1 or the complements thereof, wherein said contiguous span comprises at least 1 of the following nucleotide positions of SEQ ID No. 1;

1-481, 666-1465, 1521-67592, 67704-71118, 71185-72598, 72690-75543, 75624-81841, 81934-83019, 83406-87901, 88041-93856, 93937-97158, 97236-98962, 99086-103188, 103745-104303, 104654-105084, 105180-106682, 106781-107798, 107897-108392, 108552-114335, 114418-114491, 114594-132246, 132332-134150, 134350-145565, 145842-146332, 146775-150446, 150542-152959, 153176-155590, 155738-159701, 160466-161028, and 161453-162450,

b) a polynucleotide comprising a contiguous span of at least 12 nucleotides of SEQ ID No 4 or the complements thereof, wherein said contiguous span comprises at least 1 of the following nucleotide positions of SEQ ID No. 4;

1-208, 1307-1350, 1703-1865, 2107-2180, 2843-3333, 3871-3882, 42224276, and 5017-5579;

c) a polynucleotide having a sequence selected from the group of SEQ ID Nos. 5-28, a sequence complementary thereto or a fragment or a variant thereof;

d) a polynucleotide comprising a combination of at least two polynucleotides selected from the group consisting of SEQ ID Nos. 5-28, wherein the polynucleotides are arranged within the nucleic acid, from the 5′

end to the 3 ′

end of said nucleic acid, in the same order than in SEQ ID No. 1, and

e) a polynucleotide which encodes a polypeptide comprising a contiguous span of at least 6 amino acids of SEQ ID No. 29.

24. A host cell comprising a recombinant vector according to claim 23.

25. A non-human host animal or mammal comprising a recombinant vector according to claim 23.

26. A mammalian host cell comprising a RBP-7 gene disrupted by homologous recombination with a knock out vector, comprising a polynucleotide selected from the group consisting of:

a) a polynucleotide comprising a contiguous span of at least 12 nucleotides of SEQ ID No. 1 or the complements thereof, wherein said contiguous span comprises at least 1 of the following nucleotide positions of SEQ ID No. 1;

1-481, 666-1465, 1521-67592, 67704-71118, 71185-72598, 72690-75543, 75624-81841, 81934-83019, 83406-87901, 88041-93856, 93937-97158, 97236-98962, 99086-103188, 103745-104303, 104654-105084, 105180-106682, 106781-107798, 107897-108392, 108552-114335, 114418-114491, 114594-132246, 132332-134150, 134350-145565, 145842-146332, 146775-150446, 150542-152959, 153176-155590, 155738-159701, 160466-161028, and 161453-162450,

b) a polynucleotide comprising a contiguous span of at least 12 nucleotides of SEQ ID No. 4 or the complements thereof, wherein said contiguous span comprises at least 1 of the following nucleotide positions of SEQ ID No 4. 1-208, 1307-1350, 1703-1865, 2107-2180, 2843-3333, 3871-3882, 4222-4276, and 5017-5579,

c) a polynucleotide having a sequence selected from the group of SEQ ID Nos. 5-28, a sequence complementary thereto or a fragment or a variant thereof;

d) a polynucleotide comprising a combination of at least two polynucleotides selected from the group consisting of SEQ ID Nos 5-28, wherein the polynucleotides are arranged within the nucleic acid, from the 5′

end to the 3 ′

end of said nucleic acid, in the same order than in SEQ ID No. 1; and

e) a polynucleotide which encodes a polypeptide comprising a contiguous span of at least 6 amino acids of SEQ ID No. 29.

27. A non-human host mammal comprising a RBP-7 gene disrupted by homologous recombination with a knock out vector, comprising a polynucleotide selected from the group consisting of:

a) a polynucleotide comprising a contiguous span of at least 12 nucleotides of SEQ ID No. 1 or the complements thereof, wherein said contiguous span comprises at least 1 of the following nucleotide positions of SEQ ID No. 1;

1-481, 666-1465, 1521-67592, 67704-71118, 71185-72598, 72690-75543, 75624-81841, 81934-83019, 83406-87901, 88041-93856, 93937-97158, 97236-98962, 99086-103188, 103745-104303, 104654-105084, 105180-106682, 106781-107798, 107897-108392, 108552-114335, 114418-114491, 114594-132246, 132332-134150, 134350-145565, 145842-146332, 146775-150446, 150542-152959, 153176-155590, 155738-159701, 160466-161028, and 161453-162450;

b) a polynucleotide comprising a contiguous span of at least 12 nucleotides of SEQ ID No. 4 or the complements thereof, wherein said contiguous span comprises at least 1 of the following nucleotide positions of SEQ ID No. 4;

1-208, 1307-1350, 1703-1865, 2107-2180, 2843-3333, 3871-3882, 4222-4276, and 5017-5579;

c) a polynucleotide having a sequence selected from the group of SEQ ID Nos. 5-28, a sequence complementary thereto or a fragment or a variant thereof,

d) a polynucleotide comprising a combination of at least two polynucleotides selected from the group consisting of SEQ ID Nos 5-28, wherein the polynucleotides are arranged within the nucleic acid, from the 5′

end to the 3′

end of said nucleic acid, in the same order than in SEQ ID No 1; and

e) a polynucleotide which encodes a polypeptide comprising a contiguous span of at least 6 amino acids of SEQ ID No. 29 28 An isolated, purified, or recombinant polypeptide comprising a contiguous span of at least 6 amino acids of SEQ ID No. 29.

29. An isolated or purified antibody composition capable of selectively binding to an epitope-containing fragment of a polypeptide according to claim 28