ATM kinase modulation for screening and therapies

Details ATM kinase modulation for screening and therapies ATM kinase modulation for screening and therapies

1999-02-10

2002-05-14

Achutamurthy, Ponnathapu (Department: 1652)

Chemistry: molecular biology and microbiology

Measuring or testing process involving enzymes or...

Involving transferase

C435S194000, C435S252300, C435S325000, C435S320100

Reexamination Certificate

active

06387640

ABSTRACT:

FIELD OF THE INVENTION
The present invention relates to identification of the consensus sequence phosphorylated by ATM kinase. This, in turn, permitted identification of ATM kinase target proteins, and development of a convenient assay system for ATM kinase phosphorylation using fusion polypeptides as substrates. The assay system is adaptable to screening for ATM modulators, particularly inhibitors.
BACKGROUND OF THE INVENTION
Ataxia telangiectasia (AT) is a rare autosomal recessive multi-system disorder characterized by clinical manifestations that include progressive cerebellar ataxia, neuronal degeneration, hypersensitivity to ionizing irradiation (IR), premature aging, hypogonadism, growth retardation, immune deficiency, and an increased risk for cancer (Lavin and Shiloh, Annu. Rev. Immunol., 15:177, 1997). Cancer predisposition in AT is striking: 38% of patients develop malignancies, mainly lymphoreticular neoplasms and leukemias. But AT patients manifest acute radiosensitivity and must be treated with reduced radiation doses, and not with radiomimetic chemotherapy. AT has a worldwide frequency of 1:100,000 live births and an estimated carrier frequency of 1% in the American population. Notable concentrations of AT patients outside the United States are in Turkey, Italy, and Israel.
Cerebellar ataxia that gradually develops into general motor dysfunction is the first clinical hallmark and results from progressive loss of Purkinje cells in the cerebellum. Oculocutaneous telangiectasia (dilation of blood vessels) develops in the bulbar conjunctiva and facial skin, and is later accompanied by graying of the hair and atrophic changes in the skin. Somatic growth is retarded in most patients, and ovarian dysgenesis is typical for female patients. Among occasional endocrine abnormalities, insulin-resistant diabetes is predominant, and serum levels of alpha-fetoprotein and carcinoembryonic antigen are elevated. The thymus is either absent or vestigial, and other immunological defects include reduced levels of serum IgA, IgE or IgG2, peripheral lymphopenia, and reduced responses to viral antigens and allogeneic cells. These immunological defects cause many patients to suffer from recurrent sinopulmonary infections. The most common cause of death in AT, typically during the second or third decade of life, is from these sinopulmonary infections with or without malignancy.
The gene mutated in AT, ATM (Ataxia Telangiectasia-Mutated), encodes a 370-kD protein that is a member of a family of proteins related to phosphatidylinositol 3-kinase (PI-3-K) that have either lipid or protein kinase activity. A subset of this family with the greatest homology to ATM functions in DNA repair, DNA recombination, and cell cycle control (Savitsky et al., Science, 268:1749, 1995; Keith and Screiber, ibid., 270:50, 1995). Cell lines derived from AT patients exhibit hypersensitivity to ionizing radiation (IR) and defects in several IR-inducible cell cycle checkpoints, including a diminished irradiation-induced arrest in the G1 phase of the cell cycle mediated by the p53 tumor suppressor gene product (Kastan et al., Cell, 71:587, 1992; Morgan and Kastan, Adv. Cancer Res., 71:1, 1997). In response to DNA damage, cells with wild type ATM accumulate p53 protein and show a subsequent increase in p53 activity, whereas cells with defective ATM show a smaller increase in the amount of p53 protein in response to IR (Kastan et al., supra, Canman et al., Cancer Res., 54:5054, 1994; Khanna and Lavin, Oncogene, 8:3307, 1993). Therefore, ATM appears to act upstream of p53 in a signal transduction pathway initiated by IR.
IR induces rapid, de novo phosphorylation of endogenous p53 at two serine residues within the first 24 amino acids of the protein, one of which was identified as Ser
15
(Shieh et al., Cell, 91:325, 1997; Siliciano et al., Genes Dev., 11:3471, 1997). Phosphorylation of p53 at Ser
15
in response to DNA damage correlates with both the accumulation of total p53 protein as well as with the ability of p53 to transactivate downstream target genes in wild type cells (Siliciano et al., supra). Furthermore, phosphorylation of p53 on Ser
15
in response to IR is diminished in cell lines derived from AT patients, suggesting that ATM participates in this response (Siliciano et al., supra).
The P13-K-related protein, DNA-activated protein kinase (DNA-PK), phosphorylates p53 in vitro at two different SQ motifs, Ser
15
and Ser
37
(Lees-Miller et al., Mol. Cell Biol., 12:5041, 1992). However, cells with diminished DNA-PK activity still normally accumulate p53 protein and undergo G1 arrest in response to IR (Rathmell et al., Cancer Res., 57:68, 1997; Guialos et al, Genes Dev., 10:2038, 1996; Nacht et al., ibid., p. 2055).
The concept of inhibiting ATM for the treatment of neoplasms, particularly cancers associated with decreased p53 function, has been suggested (Morgan et al., Mol. Cell Biol. 17:2020, 1997; Hartwell and Kastan, Science, 266:1821, 1994; Kastan, New Eng. J. Med. 333:662, 1995; see also WO 98/56391, Westphal and Leder). In particular, Westphal and Leder provide genetically manipulated knock-out mice as a model for testing ATM inhibitors. This published application suggests using an inhibitory antibody to ATM, a dominant negative fragment of ATM (see also Morgan et al., supra), or an ATM antisense strategy to inhibit ATM. However, while these publications propose inhibiting ATM to enhance radiosensitivity of neoplastic cells, and screening for compounds that inhibit ATM activity, they provide no specific screening test, particularly one suitable for high through-put screening. There is no hint or suggestion in these publications of strategies for targeting the kinase activity of ATM, the nature of an ATM kinase substrate recognition sequence, or of sequences recognized specifically by ATM, but not other kinases. There is also no information about the function of other ATM target proteins besides p53.
Accordingly, there is a need in the art to understand ATM kinase specificity. There is a further need to identify ATM target proteins other than p53.
These and other needs in the art are addressed by the present invention.
SUMMARY OF THE INVENTION
The present invention relates to the identification of an ATM kinase substrate recognition consensus sequence motif, and to the identification of new ATM target proteins, which in turn has led to the discovery of unexpected and novel ATM-regulated cellular pathways.
Thus, in one embodiment, the invention advantageously provides a method for identifying an ATM kinase substrate recognition sequence in a protein. This method comprises contacting an ATM kinase with a fusion polypeptide and detecting whether binding has occurred between the ATM kinase and the fusion polypeptide. The fusion polypeptide contains a structural portion and a candidate ATM-kinase substrate recognition sequence portion. Moreover, given application of sequence comparison techniques, the invention provides a method for identifying a putative ATM target protein, by analyzing the sequence of the protein to determine whether it contains an ATM substrate recognition consensus sequence motif.
In a further embodiment, a method for identifying an ATM-regulated pathway is provided. This method comprises identifying a substrate of an ATM kinase, e.g., as described above; modulating ATM-mediated phosphorylation of the target protein comprising an ATM recognition sequence; and determining whether modulation of ATM-mediated phosphorylation of the target protein affects a cellular pathway, which would indicate that the pathway is an ATM-regulated pathway. As a corollary, the invention provides a method for modulating an ATM-regulated pathway, which comprises modulating ATM-mediated phosphorylation of a target protein comprising an ATM-kinase recognition sequence in a cell.
The methods of the invention can involve a kinase-dead ATM mutant polypeptide. Thus, in a further embodiment, the invention provides a nucleic acid encoding such a polypeptide, as well as the polypeptide itself. The invention provides a

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