Baalc expression as a diagnostic marker for acute leukemia

This application is a divisional of and claims priority to U.S. application Ser. No. 10/293,239, filed on Nov. 12, 2002, which claims priority to U.S. Provisional Application Ser. No. 60/348,210, filed Nov. 9, 2001, both of which are incorporated by reference herein in their entirety.

This invention was made, at least in part, with government support under National Institutes of Health Grant No. 5P30CA016058. The U.S. government has certain rights in the invention.

Leukemias comprise approximately 2% of adult cancers and are a heterogeneous group. There are two broad categories of leukemias. Acute leukemias arise when there is a block in the normal differentiation of cells to mature blood cells that results in large accumulations of immature cells or blasts in the blood. Examples of such cancers are acute myelogenous leukemia (AML; other names are acute myeloid leukemia and acute nonlymphocytic leukemia) and acute lymphoblastic leukemia (ALL). In chronic leukemia, on the other hand, there is unregulated proliferation of cells that have differentiated to mature blood cells. Examples of such cancers are chronic lymphocytic leukemia (CLL) and chronic myelogenous leukemia (CML). CML has a chronic phase which then progresses to a phase called blast crisis where immature, blast cells are present in the blood. Both acute and chronic leukemias involve the myeloid cells of the bone marrow, including white cells, red cells, megakaryocytes and cells of the lymphoid lineage.

The cytogenetics of many leukemias are characterized by balanced chromosomal translocations that give rise to gene rearrangements. In acute myeloid leukemia (AML) for example, about 55% of adult de novo cases have clonal cytogenetic abnormalities, many of which are specific translocations. However, in the remaining cases, no visible cytogenetic abnormalities are found, although genetic changes are detected methods other than cytogenetics. In adult acute lymphoblastic leukemia (ALL), the proportion of patients with no cytogenetic abnormality is about 31%.

Tumors of the central nervous system (CNS) comprise primary brain tumors, primary intraspinal tumors, and tumors that metastasize to the CNS. Brain tumors comprise astrocytomas, glioblastomas, medulloblastomas, and others. An extracranial pediatric tumor, neuroblastoma, arises in pluripotent neural crest cells of the sympathetic nervous system.

Prostate cancer is an epithelial cell cancer of men. Most are adenocarcinomas. Tumorigenesis progresses from normal to hyperplasic prostate to well and poorly differentiated carcinoma.

Many cancers, including leukemias, CNS and prostate cancers suffer from the problem of late detection in patients. Also, even when such cancers are detected in a patient, it is often difficult to predict lifespan of, or to determine the optimal therapy for, the particular cancer in the particular patient. However, cancers are genetic diseases that are associated with changes in cellular DNA (i.e., genetic changes). Because occurrence of such DNA changes precedes the appearance of phenotypic changes characteristic of cancer cells, it is advantageous to use detection of such early genetic changes as an aid to cancer diagnosis. Also, because a single cancer type, as identified phenotypically or pathologically, may include cancers that can be subgrouped based on classification of genetic changes therein, detection of these genetic changes may provide improved patient prognosis and selection of more efficacious therapy, based on the subgroupings.

Although the specific genetic changes associated with some cancers are known, in other cancers the associated genetic changes are not known. Even if the genetic changes are not known, it may be possible to identify additional molecular changes resulting from the genetic changes contributing to cancer. For example, a genetic change in a cancer cell may result in changes in gene expression (i.e., transcription and/or translation) of multiple genes in a cancer cell. A gene which is not normally expressed in a particular cell type may come to be expressed in cancer cells, or a gene that is expressed at low levels in normal cells may come to be expressed at high levels in cancer cells. Such gene expression changes may be diagnostically and prognostically useful alone or may be used together with already identified cancer-associated genetic and gene expression changes in multivariate analysis for purposes of prognosis and selection of effective anticancer therapy.

Therefore, it would be advantageous to identify and characterize genetic changes and gene expression changes present in cancer cells, particularly in leukemias, CNS and prostate cancers, that can be used to more effectively diagnose a specific cancer, predict its outcome in a patient, and aid in selecting an efficacious therapy.

A new gene, BAALC (Brain and Acute Leukemia, Cytoplasmic) has been identified that has eight exons, and expresses eight alternatively-spliced transcripts and six protein isoforms. The BAALC gene, while normally expressed in central nervous system (CNS) tissues, adrenal gland, thyroid and spleen, is overexpressed in subsets of leukemias, in certain CNS cancers, and in prostate cancer.

Thus, the present invention provides oligonucleotides and polynucleotides sequences identical or complementary to sequences within BAALC exons or transcripts. The oligonucleotides are used as primers and probes for detecting BAALC expression and overexpression in a biological sample obtained from a patient.

The present invention also provides polyclonal and monoclonal antibodies that specifically bind to one or more BAALC protein isoforms, as well as peptide immunogens for preparing the antibodies. The antibodies are used for detecting expression and overexpression of BAALC proteins or polypeptides in a biological sample obtained from a patient.

The present invention also provides methods of characterizing certain leukemias in a patient. One such leukemia is acute myelogenous leukemia (AML). The method comprises assaying a biological sample obtained from a patient for the presence of one or more BAALC transcripts or protein isoforms, wherein overexpressed levels of BAALC transcripts or protein isoforms indicate an aggressive form of AML. Another such leukemia is chronic myelogenous leukemia (CML). This method comprises assaying a biological sample obtained from a patient for the presence of overexpressed levels of BAALC transcripts or protein isoforms wherein overexpressed levels in the CML cells indicates the cells have entered the stage of blast crisis.

The present invention also provides methods of diagnosing and characterizing prostate tumors. The method comprises assaying a biological sample obtained from a patient for the presence of overexpressed levels of BAALC transcripts or protein.

The present invention also provides a kit for characterizing AML, CML or prostate cancer wherein the kit comprises primers containing sequences identical or complementary to sequences within specific BAALC exons. The kit may also comprise a probe containing a sequence complementary to a sequence contained within a polymerase chain reaction (PCR) product obtained using the primers.