Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2001-01-18
2004-04-20
Myers, Carla J. (Department: 1634)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S091200, C536S023500, C536S024310, C536S024330
Reexamination Certificate
active
06723506
ABSTRACT:
FIELD OF THE INVENTION
The present invention relates to oncology and identification of oncogenes and oncoproteins useful in the diagnosis, prognosis and therapy associated with neoplasia.
BACKGROUND OF THE INVENTION
Chromosome aberrations are characteristic of human cancer and include translocations, inversions, amplifications and deletions. Chromosomal translocations often generate gene fusions (i.e., fusion oncogenes) that contribute to tumorigenesis through expression of encoded oncoproteins. Some translocations fuse (i.e., physically join) promoter sequences of one gene with coding sequences of another gene leading to overexpression of wild type proto-oncoproteins. Other translocations fuse coding sequence of two genes leading to expression of chimeric oncoproteins. Chimeric fusion oncogenes/oncoproteins are specific to tumor tissue and usually to cancer type. They reproduce many aspects of cancer in animal models and are of wide interest because they define biologic pathways important in human neoplasia and are ideal targets for diagnosis and therapy.
Translocations harboring fusion oncogenes have been observed consistently in human leukemia/lymphomas and sarcomas but not in carcinomas. In fact, most chromosome abnormalities identified in carcinomas to date have consisted of deletions involving loss of growth restraining tumor suppressor genes rather than translocations involving fusion oncogenes.
The search for mechanisms underlying cancer and oncogenesis is ongoing. Understanding tumorigenesis and the reasons for uncontrolled and/or rapid cell proliferation will help researchers and clinicians develop tools for early detection, diagnosis and aggressive treatment of neoplasias.
SUMMARY OF THE INVENTION
Carcinomas are the predominant causes of cancer morbidity and death in humans. The invention relates to novel molecular markers, screening assays and therapeutic strategies for carcinoma and provides compositions and methods for diagnosing and treating carcinomas, and in some aspects particularly thyroid follicular carcinoma. The invention is premised, in part, on the discovery that PAX8 and PPAR&ggr; genomic loci are able to translocate to form fusion nucleic acid molecules and polypeptides which comprise both PAX8 and PPAR&ggr; sequences. Thus, the invention is based in part on the finding of a fusion oncogene designated PAX8-PPAR&ggr;1 (or its reciprocal PPAR&ggr;1-PAX8) in carcinoma samples. The fusion oncogene (and its reciprocal) are the result of a chromosomal translocation fusing chromosomes 2 and 3, and herein referred to as t(2;3)(q13;p25).
According to one aspect of the invention, an isolated PAX8-PPAR&ggr;1 nucleic acid molecule is provided which comprises: (a) a nucleic acid molecule which hybridizes under stringent conditions to a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5 and SEQ ID NO:22 and which codes for a PAX8-PPAR&ggr;1 polypeptide; (b) deletions, additions and substitutions of (a) which code for a respective PAX8-PPAR&ggr;1 polypeptide; (c) a nucleic acid molecule that differs from the nucleic acid molecules of (a) or (b) in codon sequence due to the degeneracy of the genetic code; and (d) complements of (a), (b) or (c). The preferred PAX8-PPAR&ggr;1 nucleic acid molecules comprise a sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5 and SEQ ID NO:22. In another embodiment, the invention provides isolated nucleic acid molecules which code for a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6 and SEQ ID NO:23.
The invention provides similar aspects which relate to the reciprocal fusion, PPAR&ggr;1-PAX8. Thus, according to one aspect of the invention, an isolated PPAR&ggr;1-PAX8 nucleic acid molecule is provided which comprises: (a) a nucleic acid molecule which hybridizes under stringent conditions to a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO:36, SEQ ID NO:37 and SEQ ID NO:38 and which codes for a PPAR&ggr;1-PAX8 polypeptide; (b) deletions, additions and substitutions of (a) which code for a respective PPAR&ggr;1-PAX8 polypeptide; (c) a nucleic acid molecule that differs from the nucleic acid molecules of (a) or (b) in codon sequence due to the degeneracy of the genetic code; and (d) complements of (a), (b) or (c). The preferred PPAR&ggr;1-PAX8 nucleic acid molecules comprise a sequence selected from the group consisting of SEQ ID NO:36, SEQ ID NO:37 and SEQ ID NO:38. In another embodiment, the invention provides isolated nucleic acid molecules which code for a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:39, SEQ ID NO:40 and SEQ ID NO:41.
According to yet another aspect of the invention, an isolated PAX8-PPAR&ggr;1 nucleic acid molecule is provided which is selected from the group consisting of: (a) a unique fragment of a nucleic acid molecule comprising a sequence selected from the group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5 and SEQ ID NO:22 (of sufficient length to represent a sequence unique within the human genome); and (b) complements of (a), provided that the unique fragment includes a sequence of contiguous nucleotides which is not identical to any sequence selected from the group consisting of: (1) sequences having the database accession numbers of Table 1 (corresponding to each SEQ ID NO) or other previously published sequences as of the date of invention or the filing date of this application, (2) complements of (1), and optionally (3) fragments of (1) and (2).
According to yet another aspect of the invention, an isolated PPAR&ggr;1-PAX8 nucleic acid molecule is provided which is selected from the group consisting of: (a) a unique fragment of a nucleic acid molecule comprising a sequence selected from the group consisting of SEQ ID NO:36, SEQ ID NO:37, and SEQ ID NO:38 (of sufficient length to represent a sequence unique within the human genome); and (b) complements of (a), provided that the unique fragment includes a sequence of contiguous nucleotides which is not identical to any sequence selected from the group consisting of: (1) sequences having the database accession numbers of Table 1 (corresponding to each SEQ ID NO)or other previously published sequences as of the date of invention or the filing date of this application, (2) complements of (1), and optionally (3) fragments of (1) and (2).
In one embodiment, the sequence of contiguous nucleotides is selected such that at least one, or at least two, or at least three, or at least four or more contiguous nucleotides derive from each of the source genes (i.e., PPAR&ggr; or PAX8).
In one embodiment, the sequence of contiguous nucleotides is selected from the group consisting of (1) at least two contiguous nucleotides nonidentical to the sequence group, (2) at least three contiguous nucleotides nonidentical to the sequence group, (3) at least four contiguous nucleotides nonidentical to the sequence group, (4) at least six contiguous nucleotides nonidentical to the sequence group, (5) at least eight contiguous nucleotides nonidentical to the sequence group, and (6) at least ten contiguous nucleotides nonidentical to the sequence group.
In another embodiment, the unique fragment has a size selected from the group consisting of at least 8 nucleotides, at least 10 nucleotides, at least 12 nucleotides, at least 14 nucleotides, at least 16 nucleotides, at least 18 nucleotides, at least 20, nucleotides, at least 22 nucleotides, at least 24 nucleotides, at least 26 nucleotides, at least 28 nucleotides, at least 30 nucleotides, at least 40 nucleotides, at least 50 nucleotides, at least 75 nucleotides, at least 100 nucleotides, at least 200 nucleotides, at least 1000 nucleotides and every integer length therebetween as if fully cited herein.
In other embodiments, the unique fragment encodes a peptide which is a fragment of a polypeptide comprising an amino acid sequence selected fro
Fletcher Jonathan A.
Kroll Todd G.
Brigham and Women's Hospital
Myers Carla J.
Sakelaris Sally A
Wolf Greenfield & Sacks P.C.
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