Claims
- 1. A method for diagnosing Noonan syndrome in a subject, which method comprises detecting a mutation in a protein tyrosine phosphatase 11 (PTPN11) gene in the subject, wherein the mutation results in increased PTPN11 expression or activity as compared to a control.
- 2. The method of claim 1, wherein the mutation is a member of the group consisting of a missense mutation, a deletion, an insertion, and both a deletion and an insertion.
- 3. The method of claim 1, wherein the mutation is in a coding region of the gene.
- 4. The method of claim 3, wherein the mutation in the coding region results in a mutation in the PTPN11 protein.
- 5. The method of claim 4, wherein the mutation in the PTPN11 protein is in an src-homology 2 (SH2) domain.
- 6. The method of claim 5, wherein the mutation in the PTPN11 protein is an amino acid substitution selected from the group consisting of
a) a G to A substitution at position 60 of SEQ ID NO: 2; b) a D to N substitution at position 61 of SEQ ID NO: 2; c) a D to G substitution at position 61 of SEQ ID NO: 2; d) a Y to D substitution at position 62 of SEQ ID NO: 2; e) a Y to C substitution at position 63 of SEQ ID NO: 2; f) an A to S substitution at position 72 of SEQ ID NO: 2; g) an A to G substitution at position 72 of SEQ ID NO: 2; h) an E to D substitution at position 76 of SEQ ID NO: 2; and i) a Q to R substitution at position 79 of SEQ ID NO: 2.
- 7. The method of claim 5, wherein the mutation in the PTPN11 protein is an amino acid substitution selected from the group consisting of
a) a T to A substitution at position 42 of SEQ ID NO: 2; b) a T to I substitution at position 73 of SEQ ID NO: 2; and c) an E to D substitution at position 139 of SEQ ID NO: 2.
- 8. The method of claim 5, wherein the mutation in the PTPN11 protein is a G to V substitution at position 60 and a deletion of D at position 61 of SEQ ID NO: 2.
- 9. The method of claim 5, wherein the mutation in the PTPN11 gene is selected from the group consisting of
a) a G to C substitution at position 179 of SEQ ID NO: 1; b) a G to A substitution at position 181 of SEQ ID NO: 1; c) an A to G substitution at position 182 of SEQ ID NO: 1; d) a T to G substitution at position 184 of SEQ ID NO: 1; e) an A to G substitution at position 188 of SEQ ID NO: 1; f) a G to T substitution at position 214 of SEQ ID NO: 1; g) a C to G substitution at position 215 of SEQ ID NO: 1; h) an G to C substitution at position 228 of SEQ ID NO: 1; and i) an A to G substitution at position 236 of SEQ ID NO: 1.
- 10. The method of claim 5, wherein the mutation in the PTPN11 gene is selected from the group consisting of
a) an A to G substitution at position 124 of SEQ ID NO: 1; b) a C to T substitution at position 218 of SEQ ID NO: 1; c) a G to C substitution at position 417 of SEQ ID NO: 1; and d) a G to T substitution at position 417 of SEQ ID NO: 1.
- 11. The method of claim 10, wherein the mutation in the PTPN11 gene is a G to T substitution at position 179 and a deletion of positions 180-182 of SEQ ID NO: 1.
- 12. The method of claim 4, wherein the mutation in the PTPN11 protein is a linker domain connecting a first SH2 domain to a second SH2 domain.
- 13. The method of claim 12, wherein the mutation is a D to A amino acid substitution at position 106 of SEQ ID NO: 2.
- 14. The method of claim 12, wherein the mutation in the PTPN11 gene is an A to C substitution at position 317 of SEQ ID NO: 1.
- 15. The method of claim 4, wherein the mutation in the PTPN11 protein is in a protein tyrosine phosphatase (PTP) domain.
- 16. The method of claim 15, wherein the mutation is an amino acid substitution selected from the group consisting of
a) an Y to C substitution at position 279 of SEQ ID NO: 2; b) an I to V substitution at position 282 of SEQ ID NO: 2; c) an F to L substitution at position 285 of SEQ ID NO: 2; d) an F to S substitution at position 285 of SEQ ID NO: 2; e) an N to D substitution at position 308 of SEQ ID NO: 2; f) an N to S substitution at position 308 of SEQ ID NO: 2; g) an I to V substitution at position 309 of SEQ ID NO: 2; h) an R to K substitution at position 501 of SEQ ID NO: 2; and i) an M to V substitution at position 504 of SEQ ID NO: 2.
- 17. The method of claim 15, wherein the mutation is an amino acid substitution selected from the group consisting of
a) a G to S substitution at position 268 of SEQ ID NO: 2; b) an N to T substitution at position 308 of SEQ ID NO: 2; c) an P to S substitution at position 491 of SEQ ID NO: 2; and d) an S to L substitution at position 502 of SEQ ID NO: 2.
- 18. The method of claim 15, wherein the mutation in the PTPN11 gene is selected from the group consisting of
a) an A to G substitution at position 836 of SEQ ID NO: 1; b) an A to G substitution at position 844 of SEQ ID NO: 1; c) a T to C substitution at position 853 of SEQ ID NO: 1; d) a T to C substitution at position 854 of SEQ ID NO: 1; e) an A to G substitution at position 922 of SEQ ID NO: 1; f) an A to G substitution at position 923 of SEQ ID NO: 1; g) an A to G substitution at position 925 of SEQ ID NO: 1; h) a G to A substitution at position 1502 of SEQ ID NO: 1; and i) an A to G substitution at position 1510 of SEQ ID NO: 1.
- 19. The method of claim 12, wherein the mutation in the PTPN11 gene is selected from the group consisting of
a) a G to A substitution at position 802 of SEQ ID NO: 1; h) an A to C substitution at position 923 of SEQ ID NO: 1; j) a C to T substitution at position 1471 of SEQ ID NO: 1; and l) a C to T substitution at position 1505 of SEQ ID NO: 1.
- 20. A kit for diagnosing Noonan syndrome, comprising
an oligonucleotide that specifically hybridizes to or adjacent to a site of mutation of a PTPN11 gene that results in increased activity of a PTPN11 protein encoded by the gene; and instructions for use.
- 21. The kit of claim 20, wherein the site of mutation comprises a nucleotide selected from the group consisting of nucleotides 179, 181, 182, 184, 188, 214, 215, 228, 236, 317, 836, 844, 853, 854, 922, 923, 925, 1502, and 1510 of SEQ ID NO: 1.
- 22. The kit of claim 20, wherein the site of mutation comprises a nucleotide selected from the group consisting of nucleotides 124, 180, 218, 417, 802, 1403, 1471, and 1505 of SEQ ID NO: 1.
- 23. The kit of claim 20, comprising at least one probe comprising the site of mutation.
- 24. The kit of claim 20, comprising a first oligonucleotide primer comprising at least 15 consecutive nucleotides of SEQ ID NO: 33, and a second oligonucleotide primer comprising at least 15 consecutive nucleotides of a sequence complementary to SEQ ID NO: 33.
- 25. The kit of claim 20, comprising a first primer comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29 and 31, and a second primer selected from the group consisting of SEQ ID NOS: 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32.
- 26. A kit for diagnosing Noonan syndrome, comprising
an antibody that specifically recognizes a mutation in a PTPN11 protein; and instructions for use.
- 27. The kit of claim 26, wherein the mutation results in an increased activity as compared to a PTPN11 protein having the amino acid sequence of SEQ ID NO: 2.
- 28. The kit of claim 26, wherein the mutation is in an SH2 domain.
- 29. The kit of claim 28, wherein the mutation is selected from the group consisting of
a) a G to A substitution at position 60 of SEQ ID NO: 2; b) a D to N substitution at position 61 of SEQ ID NO: 2; c) a D to G substitution at position 61 of SEQ ID NO: 2; d) a Y to D substitution at position 62 of SEQ ID NO: 2; e) a Y to C substitution at position 63 of SEQ ID NO: 2; f) an A to S substitution at position 72 of SEQ ID NO: 2; g) an A to G substitution at position 72 of SEQ ID NO: 2; h) an E to D substitution at position 76 of SEQ ID NO: 2; and i) a Q to R substitution at position 79 of SEQ ID NO: 2.
- 30. The kit of claim 28, wherein the mutation is selected from the group consisting of
a) a T to A substitution at position 42 of SEQ ID NO: 2; b) a G to V substitution at position 60 in combination with a deletion of position 61 of SEQ ID NO: 2; b) a T to I substitution at position 73 of SEQ ID NO: 2; and c) an E to D substitution at position 139 of SEQ ID NO: 2.
- 31. The kit of claim 26, wherein the mutation is in a linker domain connecting a first SH2 domain to a second SH2 domain.
- 32. The kit of claim 31, wherein the mutation is a D to A substitution at position 106 of SEQ ID NO: 2.
- 33. The kit of claim 26, wherein the mutation is in a PTP domain.
- 34. The kit of claim 33, wherein the mutation is selected from the group consisting of
a) an Y to C substitution at position 279 of SEQ ID NO: 2; b) an I to V substitution at position 282 of SEQ ID NO: 2; c) an F to L substitution at position 285 of SEQ ID NO: 2; d) an F to S substitution at position 285 of SEQ ID NO: 2; e) an N to D substitution at position 308 of SEQ ID NO: 2; f) an N to S substitution at position 308 of SEQ ID NO: 2; g) an I to V substitution at position 309 of SEQ ID NO: 2; h) an R to K substitution at position 501 of SEQ ID NO: 2; and i) an M to V substitution at position 504 of SEQ ID NO: 2.
- 35. The kit of claim 33, wherein the mutation is selected from the group consisting of
a) a G to S substitution at position 268 of SEQ ID NO: 2; b) an N to T substitution at position 308 of SEQ ID NO: 2; c) an P to S substitution at position 491 of SEQ ID NO: 2; and d) an S to L substitution at position 502 of SEQ ID NO: 2.
- 36. A method for diagnosing Noonan syndrome in a subject, which method comprises assessing the level of expression or activity of a PTPN11 protein in the test subject and comparing it to the level of expression or activity in a control subject, wherein an increased expression or basal activity of the PTPN11 protein in the test subject compared to the control subject is indicative of Noonan syndrome.
- 37. The method of claim 36, wherein the level of expression is assessed by determining the amount of mRNA that encodes the PTPN11 protein in a biological sample.
- 38. The method of claim 36, wherein the level of expression of PTPN11 is assessed by determining the concentration of PTPN11 protein in a biological sample.
- 39. The method of claim 36, wherein the level of activity is assessed by determining the level of phosphatase activity of the protein.
- 40. A method for diagnosing Noonan syndrome in a subject, which method comprises assessing the level of activity of a PTPN11 signal transduction pathway in a test subject and comparing it to the level of activity in a control subject, wherein increased activity of the pathway in the test subject compared to the control subject is indicative of Noonan syndrome.
- 41. The method according to claim 4, wherein the level of activity of the pathway is assessed by assessing an increase in the level of expression or activity of a PTPN11 protein.
- 42. The method according to claim 40, wherein the level of activity of the pathway is assessed by assessing an increase in the level of expression or activity of an ERK protein.
- 43. The method according to claim 42, wherein an increase in the level of expression or activity of the ERK protein is assessed by assessing kinase activity.
- 44. A method for treating Noonan syndrome in, a patient, which method comprises administering to the patient in need of such treatment an effective amount of an agent that modulates the expression or activity of a PTPN11 protein, in association with a pharmaceutically acceptable carrier.
- 45. The method of claim 44, wherein the PTPN11 protein comprises the amino acid sequence of SEQ ID NO: 2.
- 46. The method of claim 44, wherein the agent is a PTPN11 antisense nucleic acid.
- 47. The method of claim 46, wherein the antisense nucleic acid hybridizes to a segment of SEQ ID NO: 1 comprising at least one nucleotide substitution selected from the group consisting of
a) a G to C substitution at position 179 of SEQ ID NO: 1; b) a G to A substitution at position 181 of SEQ ID NO: 1; c) an A to G substitution at position 182 of SEQ ID NO: 1; d) a T to G substitution at position 184 of SEQ ID NO: 1; e) an A to G substitution at position 188 of SEQ ID NO: 1; f) a G to T substitution at position 214 of SEQ ID NO: 1; g) a C to G substitution at position 215 of SEQ ID NO: 1; h) an G to C substitution at position 228 of SEQ ID NO: 1; i) an A to G substitution at position 236 of SEQ ID NO: 1; and complementary segments thereof.
- 48. The method of claim 46, wherein the antisense nucleic acid hybridizes to a segment of SEQ ID NO: 1 comprising at least one nucleotide substitution selected from the group consisting of
a) an A to G substitution at position 124 of SEQ ID NO: 1; b) a C to T substitution at position 218 of SEQ ID NO: 1; c) a G to C substitution at position 417 of SEQ ID NO: 1; d) a G to T substitution at position 417 of SEQ ID NO: 1; and complementary segments thereof.
- 49. The method of claim 46, wherein the antisense nucleic acid hybridizes to a segment of SEQ ID NO: 1 comprising a G to T substitution at position 179 and a deletion of positions 180-182.
- 50. . The method of claim 46, wherein the antisense nucleic acid hybridizes to a segment of SEQ ID NO: 1 comprising at least one nucleotide substitution selected from the group consisting of
a) an A to G substitution at position 836 of SEQ ID NO: 1; b) an A to G substitution at position 844 of SEQ ID NO: 1; c) a T to C substitution at position 853 of SEQ ID NO: 1; d) a T to C substitution at position 854 of SEQ ID NO: 1; e) an A to G substitution at position 922 of SEQ ID NO: 1; f) an A to G substitution at position 923 of SEQ ID NO: 1; g) an A to G substitution at position 925 of SEQ ID NO: 1; h) a G to A substitution at position 1502 of SEQ ID NO: 1; i) an A to G substitution at position 1510 of SEQ ID NO: 1; and complementary sequences thereof.
- 51. The method of claim 46, wherein the antisense nucleic acid hybridizes to a segment of SEQ ID NO: 1 comprising at least one nucleotide substitution selected from the group consisting of
a) an G to A substitution at position 802 of SEQ ID NO: 1; h) an A to C substitution at position 923 of SEQ ID NO: 1; j) a C to T substitution at position 1471 of SEQ ID NO: 1; and l) a C to T substitution at position 1505 of SEQ ID NO: 1. and complementary segments thereof.
- 52. The method of claim 44, wherein the agent inhibits PTPN11 activity by blocking a PTP domain.
- 53. The method of claim 51, wherein the agent is an anti-PTPN11 inhibitory antibody.
- 54. The method of claim 53, wherein the antibody specifically recognizes a PTPN11 amino acid sequence comprising mutation selected from the group consisting of:
a) a G to A substitution at position 60 of SEQ ID NO: 2; b) a D to N substitution at position 61 of SEQ ID NO: 2; c) a D to G substitution at position 61 of SEQ ID NO: 2; d) a Y to D substitution at position 62 of SEQ ID NO: 2; e) a Y to C substitution at position 63 of SEQ ID NO: 2; f) an A to S substitution at position 72 of SEQ ID NO: 2; g) an A to G substitution at position 72 of SEQ ID NO: 2; h) an E to D substitution at position 76 of SEQ ID NO: 2; i) a Q to R substitution at position 79 of SEQ ID NO: 2; j) a D to A substitution at position 106 of SEQ ID NO: 2; k) a Y to C substitution at position 279 of SEQ ID NO: 2; l) an I to V substitution at position 282 of SEQ ID NO: 2; m) an F to L substitution at position 285 of SEQ ID NO: 2; n) an F to S substitution at position 285 of SEQ ID NO: 2; o) an N to D substitution at position 308 of SEQ ID NO: 2; p) an N to S substitution at position 308 of SEQ ID NO: 2; q) an I to V substitution at position 309 of SEQ ID NO: 2; r) an R to K substitution at position 501 of SEQ ID NO: 2; and s) an M to V substitution at position 504 of SEQ ID NO: 2.
- 55. The method of claim 53, wherein the antibody specifically recognizes a PTPN11 amino acid sequence comprising an amino acid substitution selected from the group consisting of:
a) a T to A substitution at position 42 of SEQ ID NO: 2; b) a G to V substitution at position 60 in combination with a deletion of position 61 of SEQ ID NO: 2; c) a T to I substitution at position 73 of SEQ ID NO: 2; d) an E to D substitution at position 139 of SEQ ID NO: 2; e) a G to S substitution at position 268 of SEQ ID NO: 2; f) an N to T substitution at position 308 of SEQ ID NO: 2; g) an P to S substitution at position 491 of SEQ ID NO: 2; and h) an S to L substitution at position 502 of SEQ ID NO: 2.
- 56. An isolated PTPN11 variant comprising a mutation resulting in increased level of PTPN11 activity.
- 57. The isolated PTPN11 variant of claim 56, comprising an amino acid substitution in a region selected from the group consisting of an N-SH2 domain, C-SH2 domain, PTP domain, and a region between an N-SH2 and a C-SH2 domain.
- 58. The isolated PTPN11 variant of claim 57, wherein the amino acid substitution is selected from the group consisting of
a) a G to A substitution at position 60 of SEQ ID NO: 2; b) a D to N substitution at position 61 of SEQ ID NO: 2; c) a D to G substitution at position 61 of SEQ ID NO: 2; d) a Y to D substitution at position 62 of SEQ ID NO: 2; e) a Y to C substitution at position 63 of SEQ ID NO: 2; f) an A to S substitution at position 72 of SEQ ID NO: 2; g) an A to G substitution at position 72 of SEQ ID NO: 2; h) an E to D substitution at position 76 of SEQ ID NO: 2; i) a Q to R substitution at position 79 of SEQ ID NO: 2; j) a D to A substitution at position 106 of SEQ ID NO: 2; k) an Y to C substitution at position 279 of SEQ ID NO: 2; l) an I to V substitution at position 282 of SEQ ID NO: 2; m) an F to L substitution at position 285 of SEQ ID NO: 2; n) an F to S substitution at position 285 of SEQ ID NO: 2; o) an N to D substitution at position 308 of SEQ ID NO: 2; p) an N to S substitution at position 308 of SEQ ID NO: 2; q) an I to V substitution at position 309 of SEQ ID NO: 2; r) an R to K substitution at position 501 of SEQ ID NO: 2; and s) an M to V substitution at position 504 of SEQ ID NO: 2.
- 59. The isolated PTPN11 variant of claim 57, wherein the amino acid substitution is selected from the group consisting of
a) a T to A substitution at position 42 of SEQ ID NO: 2; b) a G to V substitution at position 60 in combination with a deletion of position 61 of SEQ ID NO: 2; c) a T to I substitution at position 73 of SEQ ID NO: 2; d) an E to D substitution at position 139 of SEQ ID NO: 2; e) a G to S substitution at position 268 of SEQ ID NO: 2; f) an N to T substitution at position 308 of SEQ ID NO: 2; g) an P to S substitution at position 491 of SEQ ID NO: 2; and h) an S to L substitution at position 502 of SEQ ID NO: 2.
- 60. An isolated cell comprising a vector, which vector comprises a nucleic acid encoding the PTPN11 variant of claim 58, operatively associated with an expression control sequence.
- 61. The cell of claim 60, selected from a prokaryotic cell and an eukaryotic cell.
- 62. An isolated cell comprising a vector, which vector comprises a nucleic acid encoding the PTPN11 variant of claim 59, operatively associated with an expression control sequence.
- 63. The cell of claim 62, selected from a prokaryotic cell and an eukaryotic cell.
- 64. An isolated nucleic acid encoding the PTPN11 variant of claim 58.
- 65. An isolated oligonucleotide which specifically hybridizes to the nucleic acid of claim 64.
- 66. An isolated nucleic acid encoding the PTPN11 variant of claim 59.
- 67. An isolated oligonucleotide which specifically hybridizes to the nucleic acid of claim 66.
Parent Case Info
[0001] This application claims priority from U.S. Provisional Application Serial No. 60/326,532, filed Oct. 1, 2001, which is hereby incorporated by reference in its entirety.
Provisional Applications (1)
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Number |
Date |
Country |
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60326532 |
Oct 2001 |
US |