EP1127062A1 - Molecules associees au lymphome et leurs utilisations - Google Patents

Molecules associees au lymphome et leurs utilisations

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Publication number
EP1127062A1
EP1127062A1 EP99956778A EP99956778A EP1127062A1 EP 1127062 A1 EP1127062 A1 EP 1127062A1 EP 99956778 A EP99956778 A EP 99956778A EP 99956778 A EP99956778 A EP 99956778A EP 1127062 A1 EP1127062 A1 EP 1127062A1
Authority
EP
European Patent Office
Prior art keywords
bal
nucleic acid
polypeptide
protein
seq
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP99956778A
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German (de)
English (en)
Other versions
EP1127062A4 (fr
Inventor
Margaret Shipp
Ricardo Aguiar
Yoshi Yakushijin
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Dana Farber Cancer Institute Inc
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Dana Farber Cancer Institute Inc
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Application filed by Dana Farber Cancer Institute Inc filed Critical Dana Farber Cancer Institute Inc
Publication of EP1127062A1 publication Critical patent/EP1127062A1/fr
Publication of EP1127062A4 publication Critical patent/EP1127062A4/fr
Withdrawn legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals

Definitions

  • DLB-CL Diffuse large B-cell lymphoma
  • DLB-CL Diffuse large B-cell lymphoma
  • DLB-CL is the most common non-Hodgkin's lymphoma in adults.
  • DLB-CL is curable in approximately 40% of patients, the majority of patients progress and die of their disease (Shipp et al. Non-Hodgkin's Lymphomas. In DeVita (ed): Principles and Practice of Oncology, 5th Edition, Philadelphia, J.B. Lippincott Company, pp. 2165-2220, 1997). Additional advancements in the treatment of this aggressive but potentially curable non-Hodgkin's lymphoma are likely to require a more precise understanding of the disease's cellular and molecular bases.
  • the present invention is based, at least in part, on the discovery of novel molecules which are differentially expressed in tumors from patients with "high risk” fatal DLB-CL disease or "low risk” cured DLB-CL. Their differentially expressed gene products are referred to herein as the "B-aggressive lymphoma” (“BAL”) nucleic acid and protein.
  • BAL B-aggressive lymphoma
  • the BAL molecules of the present invention are useful as modulating agents for regulating a variety of cellular processes.
  • this invention provides isolated nucleic acid molecules encoding BAL proteins or biologically active portions thereof, as well as nucleic acid fragments suitable as primers or hybridization probes for the detection of B AL-encoding nucleic acids.
  • a BAL nucleic acid molecule of the invention is at least
  • nucleotide sequence e.g., to the entire length of the nucleotide sequence shown in SEQ ID NOJ, 3, 4, or 6.
  • the isolated nucleic acid molecule includes the nucleotide sequence shown SEQ ID NO: 1 or 3, or a complement thereof. In another embodiment, the nucleic acid molecule includes SEQ ID NOJ and nucleotides 1-228 of SEQ ID NOJ. In another embodiment, the nucleic acid molecule includes SEQ ID NOJ and nucleotides 2791-3243 of SEQ ID NOJ. In another preferred embodiment, the nucleic acid molecule consists of the nucleotide sequence shown in SEQ ID NO:l or 3.
  • the nucleic acid molecule includes a fragment of at least 607 nucleotides (e.g., 607 contiguous nucleotides) of the nucleotide sequence of SEQ ID NO:l or 3, or a complement thereof.
  • the isolated nucleic acid molecule includes the nucleotide sequence shown SEQ ID NO:4 or 6, or a complement thereof. In another embodiment, the nucleic acid molecule includes SEQ ID NO: 6 and nucleotides 1-170 of SEQ ID NO:4. In another embodiment, the nucleic acid molecule includes SEQ ID NO:6 and nucleotides 2649-3024 of SEQ ID NO:4. In another preferred embodiment, the nucleic acid molecule consists of the nucleotide sequence shown in SEQ ID NO:4 or 6.
  • the nucleic acid molecule includes a fragment of at least 452 nucleotides (e.g., 452 contiguous nucleotides) of the nucleotide sequence of SEQ ID NO:4, SEQ ID NO:6, or a complement thereof.
  • a BAL nucleic acid molecule includes a nucleotide sequence encoding a protein having an amino acid sequence sufficiently homologous to the amino acid sequence of SEQ ID NOJ or 5.
  • a BAL nucleic acid molecule includes a nucleotide sequence encoding a protein having an amino acid sequence at least 50%, 55%, 60%, 62%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%o or more homologous to the entire length of the amino acid sequence of SEQ ID NOJ or 5.
  • an isolated nucleic acid molecule encodes the amino acid sequence of human BAL.
  • the nucleic acid molecule includes a nucleotide sequence encoding a protein having the amino acid sequence of SEQ ID NOJ or 5.
  • the nucleic acid molecule is at least 452 or 607 nucleotides in length.
  • the nucleic acid molecule is at least 452 or 607 nucleotides in length and encodes a protein having a BAL activity (as described herein).
  • Another embodiment of the invention features nucleic acid molecules, preferably
  • BAL nucleic acid molecules which specifically detect BAL nucleic acid molecules relative to nucleic acid molecules encoding non-BAL proteins.
  • a nucleic acid molecule is at least 300-350, 350-400, 400-450, 452, 452-500, 500-550, 550-600, 607 or more nucleotides in length and hybridizes under stringent conditions to a nucleic acid molecule comprising the nucleotide sequence shown in SEQ ID NOJ or 4 or a complement thereof.
  • the nucleic acid molecules are at least 15 (e.g., contiguous) nucleotides in length and hybridize under stringent conditions to nucleotides
  • nucleic acid molecules comprise nucleotides 1-333, 351-385, 463- 824, 931-1082, or 3232-3244 of SEQ ID NOJ.
  • the nucleic acid molecules are at least 15 (e.g., contiguous) nucleotides in length and hybridize under stringent conditions to nucleotides 1-39 or 57-1841 of SEQ ID NO:4. In other preferred embodiments, the nucleic acid molecules comprise nucleotides 1-39 or 57-1841 of SEQ ID NO:4. In other preferred embodiments, the nucleic acid molecule encodes a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NOJ or 5, wherein the nucleic acid molecule hybridizes to a nucleic acid molecule comprising SEQ ID NOJ, 3, 4, or 6 under stringent conditions. Another embodiment of the invention provides an isolated nucleic acid molecule which is antisense to a BAL nucleic acid molecule, e.g., the coding strand of a BAL nucleic acid molecule.
  • Another aspect of the invention provides a vector comprising a BAL nucleic acid molecule.
  • the vector is a recombinant expression vector.
  • the invention provides a host cell containing a vector of the invention.
  • the invention provides a host cell containing a nucleic acid molecule of the invention.
  • the invention also provides a method for producing a protein, preferably a BAL protein, by culturing in a suitable medium, a host cell, e.g., a mammalian host cell such as a non-human mammalian cell, of the invention containing a recombinant expression vector, such that the protein is produced.
  • the isolated protein preferably a BAL protein
  • the isolated protein includes at least one proline rich domain.
  • the isolated protein, preferably a BAL protein includes at least one proline rich domain and at least one tyrosine phosphorylation site.
  • the protein, preferably a BAL protein includes at least one proline rich domain, at least one tyrosine phosphorylation site, and has an amino acid sequence at least about 50%, 55%, 60%, 62%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% or more homologous to the amino acid sequence of SEQ ID NOJ or 5.
  • the protein preferably a BAL protein
  • the protein includes at least one proline rich domain, at least one tyrosine phosphorylation site, and plays a role in the pathogenesis of non-Hodgkin's lymphoma.
  • the protein preferably a BAL protein
  • the protein includes at least one proline rich domain, at least one tyrosine phosphorylation site, and is encoded by a nucleic acid molecule having a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO:l, 3, 4, or 6.
  • the invention features BAL proteins which are produced by recombinant DNA techniques.
  • a BAL protein or polypeptide can be synthesized chemically using standard peptide synthesis techniques, based on the amino acid sequence of SEQ ID NOJ or 5.
  • the invention features fragments of the protein having the amino acid sequence of SEQ ID NOJ or 5, wherein the fragment comprises at least 15 amino acids (e.g., contiguous amino acids) of the amino acid sequence of SEQ ID NOJ or 5.
  • the protein preferably a BAL protein, has the amino acid sequence of SEQ ID NOJ or 5, respectively.
  • the invention features an isolated protein, preferably a
  • BAL protein which is encoded by a nucleic acid molecule consisting of a nucleotide sequence at least about 50%, 55%, 60%, 65%, 70%, 72%, 75%, 80%, 85%, 90%, 95%, 98% or more homologous to a nucleotide sequence of SEQ ID NOJ, 3, 4, or 6, or a complement thereof.
  • This invention further features an isolated protein, preferably a BAL protein, which is encoded by a nucleic acid molecule consisting of a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO:l, 3, 4, or 6, or a complement thereof.
  • the proteins of the present invention or portions thereof, e.g., biologically active portions thereof, can be operatively linked to a non-BAL polypeptide (e.g., heterologous amino acid sequences) to form fusion proteins.
  • the invention further features antibodies, such as monoclonal or polyclonal antibodies, that specifically bind proteins of the invention, preferably BAL proteins.
  • the BAL proteins or biologically active portions thereof can be incorporated into pharmaceutical compositions, which optionally include pharmaceutically acceptable carriers.
  • the present invention provides a method for detecting the presence of a BAL nucleic acid molecule, protein or polypeptide in a biological sample by contacting the biological sample with an agent capable of detecting a BAL nucleic acid molecule, protein or polypeptide such that the presence of a BAL nucleic acid molecule, protein or polypeptide is detected in the biological sample.
  • the present invention provides a method for detecting the presence of BAL activity in a biological sample by contacting the biological sample with an agent capable of detecting an indicator of BAL activity such that the presence of BAL activity is detected in the biological sample.
  • the invention provides a method for modulating BAL activity comprising contacting a cell capable of expressing BAL with an agent that modulates BAL activity such that BAL activity in the cell is modulated.
  • the agent inhibits BAL activity.
  • the agent stimulates BAL activity.
  • the agent is an antibody that specifically binds to a BAL protein.
  • the agent modulates expression of BAL by modulating transcription of a BAL gene or translation of a BAL mRNA.
  • the agent is a nucleic acid molecule having a nucleotide sequence that is antisense to the coding strand of a BAL mRNA or a BAL gene.
  • the methods of the present invention are used to treat a subject having a disorder characterized by aberrant BAL protein or nucleic acid expression or activity, e.g., non-Hodgkin's lymphoma, by administering an agent which is a BAL modulator to the subject.
  • the BAL modulator is a BAL protein.
  • the BAL modulator is a BAL nucleic acid molecule.
  • the BAL modulator is a peptide, peptidomimetic, or other small molecule.
  • the disorder characterized by aberrant BAL protein or nucleic acid expression is a proliferative disorder, e.g., non-Hodgkin's lymphoma.
  • the present invention also provides a diagnostic assay for identifying the presence or absence of a genetic alteration characterized by at least one of (i) aberrant modification or mutation of a gene encoding a BAL protein; (ii) mis-regulation of the gene; and (iii) aberrant post-translational modification of a BAL protein, wherein a wild- type form of the gene encodes a protein with a BAL activity.
  • the invention provides a method for producing or identifying a compound that binds to or modulates the activity of a BAL protein, by providing an indicator composition comprising a BAL protein having BAL activity, contacting the indicator composition with a test compound, and determining the effect of the test compound on BAL activity in the indicator composition to produce or identify a compound that modulates the activity of a BAL protein.
  • Figure 1 depicts the cDNA sequence and predicted amino acid sequence of human BAL.
  • the nucleotide sequence corresponds to nucleic acids 1 to 3243 of SEQ ID NOJ .
  • the amino acid sequence corresponds to amino acids 1 to 826 of SEQ ID NO: 2.
  • the coding region without the 5' and 3' untranslated regions of the human BAL gene is shown in SEQ ID NOJ.
  • Figure 2 depicts the cDNA sequence and predicted amino acid sequence of murine BAL.
  • the nucleotide sequence corresponds to nucleic acids 1 to 3024 of SEQ ID NO:4.
  • the amino acid sequence corresponds to amino acids 1 to 826 of SEQ ID NO: 5.
  • the coding region without the 5' and 3' untranslated regions of the murine BAL gene is shown in SEQ ID NO:6.
  • Figure 3 depicts an alignment of the human BAL protein with the murine BAL protein using the ALIGN program (version 2.0), a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 2.
  • Figure 4 depicts an alignment of the human BAL nucleic acid molecule with the murine BAL nucleic acid molecule using the ALIGN program (version 2.0), a PAM120 weight residue table, a gap length penalty of 16 and a gap penalty of 4.
  • Figure 5 depicts a northern blot analysis of total RNA from 5 DLB-CL cell lines, 4 "high-risk” and 5 "low-risk” primary tumors, and 2 pairs of normal B-splenocytes, with or without Ig-activation.
  • a band of ⁇ 3Jkb (arrow), corresponding to the BAL message, is detected at high levels in only one of the cell lines (DHL-7), in the "high- risk” tumors and Ig-activated splenocytes.
  • BAL transcripts are less abundant in the "low-risk” primary tumors.
  • BAL is expressed at lower levels in the non- activated B-cells.
  • the ⁇ -actin blot demonstrates that loading does not account for the differences in BAL expression.
  • Figure 6 depicts a northern blot comparing BAL transcripts in a tumor derived from a DLB-CL cell line grown in SCID mouse and the parental suspension cells. BAL is expressed at significantly higher levels in the tumor derived RNA than in the parental cell line. The ⁇ -actin blot demonstrates that loading does not account for the observed differences.
  • FIG. 7 depicts a diagrammatic representation of BAL cDNA and protein structure.
  • Two alternatively spliced BAL cDNAs of 3243 bp (BAL L , long) and 3138 bp (BAL S , short) encode previously uncharacterized 854 aa and 819 aa proteins.
  • the alternatively spliced region and the start and stop codons are indicated in BAL cDNA.
  • the region of partial homology to the non-histone region of histone macroH2A and the potential CRK/CRK-1 binding sites (YHVL, YSVP) and proline-rich region are also highlighted.
  • Figure 8 depicts a northern blot analysis of BAL transcripts in multiple human tissues.
  • BAL transcripts are most abundant in analyzed lymphoid/hematopoietic tissues (spleen, lymph node, fetal liver and peripheral blood) and several non-hematopoietic organs (heart, skeletal muscle and colon).
  • Figure 9 depicts FISH analysis of a normal human metaphase with genomic PAC clones encompassing the BAL locus.
  • the top panel shows the Giemsa-banded metaphase.
  • the green signals represent the BAL-PAC clones hybridized to the two normal chromosome 3q21.
  • Figure 10 depicts sensitivity of the BAL semi-quantitative duplex RT-PCR.
  • the abundance of BAL in a given sample was determined by comparing the intensity of co- amplified BAL and control (ABL) PCR products by scanning densitometry.
  • the sensitivity of the duplex PCR was determined by mixing fixed amounts of cDNAs from a BAL negative and a BAL positive DLB-CL cell line to mimic BAL losses of 10%- 100% (lower panel). When the ratio of BAL/ ABL signals was plotted against the percentage of BAL lost in a given sample, the data yield a straight line and a r 2 value of 0.967 (top panel).
  • Figure 12 is a graph depicting BAL expression as determined by the duplex PCR experiments (quantified with scanning densitometry).
  • Figure 13 depicts the results from a western blot analysis of aggressive lymphoma transfectants expressing pEGFP vector only or pEGFP-BAL s .
  • Figure 14 is a graph depicting the cell migration of pEGFP vector only or pEGFP-BAL s transfectants.
  • the present invention is based, at least in part, on the discovery of novel molecules, referred to herein as BAL nucleic acid and protein molecules which are differentially expressed in malignancies such as lymphoma, e.g., non-Hodgkin's lymphoma.
  • BAL nucleic acid and protein molecules which are differentially expressed in malignancies such as lymphoma, e.g., non-Hodgkin's lymphoma.
  • the newly identified BAL nucleic acid and protein molecules can be used to identify cells exhibiting or predisposed to a malignancy such as lymphoma, e.g., non- Hodgkin's lymphoma, thereby diagnosing subjects having, or prone to developing such disorders.
  • a "malignancy” includes a cancerous uncontrolled growth of cells in an area of the body. Malignant cancers are typically classified by their microscopic appearance and the type of tissue from which they arise. Examples of malignancies include carcinomas, sarcomas, myelomas, chondrosarcomas, adenosarcomas, angiosarcomas, neuroblastomas, gliomas, medulloblastomas, erythroleukemias, and myelogenous leukemias.
  • a "lymphoma” includes a malignant neoplastic disorder of lymphoreticular tissue which produces a distinct tumor mass.
  • Lymphomas include tumors derived from the lymphoid lineage. Lymphomas usually arise in lymph nodes, the spleen, or other areas rich in lymphoid tissue. Lymphomas are typically subclassified as Hodgkin's disease and Non-Hodgkin's lymphomas, e.g. , Burkitt's lymphoma, large-cell lymphoma, and follicular lymphoma.
  • differential expression includes both quantitative as well as qualitative differences in the temporal and/or cellular expression pattern of a gene, e.g., the BAL gene, among, for example, normal cells and cells from patients with "high risk” fatal DLB-CL disease or "low risk” cured DLB-CL.
  • Genes which are differentially expressed can be used as part of a prognostic or diagnostic marker for the evaluation of subjects at risk for developing a malignancy such as a lymphoma, e.g., non-Hodgkin's lymphoma.
  • a lymphoma e.g., non-Hodgkin's lymphoma.
  • the progression state or the aggressiveness of the disorder can be evaluated. Methods for detecting the differential expression of a gene are described herein.
  • the BAL molecules comprise a family of molecules having certain conserved structural and functional features.
  • family when referring to the protein and nucleic acid molecules of the invention is intended to mean two or more proteins or nucleic acid molecules having a common structural domain or motif and having sufficient amino acid or nucleotide sequence homology as defined herein.
  • family members can be naturally or non-naturally occurring and can be from either the same or different species.
  • a family can contain a first protein of human origin, as well as other, distinct proteins of human origin or alternatively, can contain homologues of non-human origin.
  • Members of a family may also have common functional characteristics.
  • the family of BAL proteins comprise at least one "proline rich domain '
  • the term "proline rich domain” includes an amino acid sequence of about 4-6 amino acid residues in length having the general sequence X-Pro- X-X-Pro-X (where X can be any amino acid).
  • Proline rich domains are usually located in a helical structure and bind through hydrophobic interactions to SH3 domains. SH3 domains recognize proline rich domains in both forward and reverse orientations. Proline rich domains are described in, for example, Sattler M. et al., Leukemia (1998) 12:637-644, the contents of which are incorporated herein by reference.
  • BAL proteins of the invention preferably include at least one proline rich domain, but may contain two or more.
  • Amino acid residues 781-786 of the human BAL and amino acid residues 748- 753 of the murine BAL comprise proline rich domains.
  • a BAL protein of the present invention is identified based on the presence of at least one "tyrosine phosphorylation site" in the protein or corresponding nucleic acid molecule.
  • tyrosine phosphorylation site includes an amino acid sequence of about 4 amino acid residues in length having the general sequence Tyr-X-X-X (where X can be any amino acid).
  • the tyrosine in this domain is phosphorylated in response to a cellular stimulus, for example, in response to a hematopoietic growth factor (e.g., thrombopoietin, erythropoietin, or steel factor) stimulation.
  • Tyrosine phosphorylation of cellular proteins plays a major role in cell signaling, e.g., hematopoietic cell signaling.
  • Tyrosine phosphorylation sites are described in, for example, Sattler M. et al., Leukemia (1998) 12:637-644, the contents of which are incorporated herein by reference.
  • BAL proteins of the invention include at least one or two tyrosine phosphorylation sites, but may contain three or more. Amino acid residues 392-395 and 495-498 of the human BAL comprise tyrosine phosphorylation sites.
  • a BAL protein of the present invention is identified based on the presence of at least one "rod domain" in the protein or corresponding nucleic acid molecule.
  • the term "rod domain” includes an ⁇ -helical, filament forming structure that is made up of smaller repeating structures. The smallest repeating structure may contain seven amino acids in which small, generally hydrophobic amino acids are typically found in the first and fourth positions of the repeat. The seven amino acids form two turns of an ⁇ -helix and the first and fourth positions fall in the hydrophobic interior of the ⁇ -helix.
  • Rod domains in alpha and beta cardiac myosin are described in, for example, Warrick et al. (1987) Annual Rev. Cell Biol. 3:379-421.
  • a BAL protein of the present invention is identified based on the presence of at least one " ⁇ -helical region" in the protein or corresponding nucleic acid molecule that is homologous to the ⁇ -helical region of moesin, the most abundant ezrin-radixin-moesin (ERM) protein in lymphocytes.
  • ⁇ -helical region includes an amino acid sequence of about 10 to about 20 amino acids in length that forms an ⁇ -helix.
  • the ⁇ -helical region of ezrin-radixin-moesin (ERM) proteins is described in, for example, Bretscher (1999) Current Biology 8(12):721-4.
  • isolated proteins of the present invention preferably BAL proteins, have an amino acid sequence sufficiently homologous to the amino acid sequence of SEQ ID NOJ or 5 or are encoded by a nucleotide sequence sufficiently homologous to SEQ ID NOJ, 3, 4, or 6.
  • the term "sufficiently homologous" refers to a first amino acid or nucleotide sequence which contains a sufficient or minimum number of identical or equivalent (e.g., an amino acid residue which has a similar side chain) amino acid residues or nucleotides to a second amino acid or nucleotide sequence such that the first and second amino acid or nucleotide sequences share common structural domains or motifs and/or a common functional activity.
  • amino acid or nucleotide sequences which share common structural domains have at least 30%, 40%, or 50% homology, preferably 60% homology, more preferably 70%-80%, and even more preferably 90-95% homology across the amino acid sequences of the domains and contain at least one and preferably two structural domains or motifs, are defined herein as sufficiently homologous.
  • amino acid or nucleotide sequences which share at least 30%, 40%, or 50%, preferably 60%, more preferably 70-80%, or 90-95% homology and share a common functional activity are defined herein as sufficiently homologous.
  • BAL activity refers to an activity exerted by a BAL protein, polypeptide or nucleic acid molecule on a BAL responsive cell or on a BAL protein substrate, as determined in vivo, ex vivo, or in vitro, according to standard techniques.
  • a BAL activity is a direct activity, such as an association with a BAL-target molecule.
  • a "target molecule” or “binding partner” is a molecule with which a BAL protein binds or interacts in nature, such that BAL-mediated function is achieved.
  • a BAL target molecule can be a non-BAL molecule or a BAL protein or polypeptide of the present invention.
  • a BAL target molecule is a BAL ligand.
  • a BAL activity is an indirect activity, such as a cellular signaling activity mediated by interaction of the BAL protein with a BAL ligand.
  • BAL activities include modulation of cellular adhesion and modulation of the aggressiveness or severity of a malignancy such as DLB-CL.
  • BAL activities are described herein.
  • another embodiment of the invention features isolated BAL proteins and polypeptides having a BAL activity.
  • Preferred proteins are BAL proteins having at least one tyrosine phosphorylation site and, preferably, a BAL activity.
  • Other preferred proteins are BAL proteins having at least one proline rich domain and, preferably, a BAL activity.
  • BAL proteins having at least one tyrosine phosphorylation site and/or at least one proline rich domain, and are, preferably, encoded by a nucleic acid molecule having a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NOJ, 3, 4, or 6.
  • the nucleotide sequence of the isolated human BAL cDNA and the predicted amino acid sequence of the human BAL polypeptide are shown in Figure 1 and in SEQ ID NOsJ and 2, respectively.
  • the human BAL gene which is approximately 3244 nucleotides in length, encodes a protein having a molecular weight of approximately 95 kD and which is approximately 826 amino acid residues in length.
  • BAL transcripts were most abundant in lymphoid organs (spleen, lymph node, fetal liver, and peripheral blood) and several additional non-hematopoietic organs (heart, skeletal muscle and colon).
  • nucleotide sequence of the isolated murine BAL cDNA and the predicted amino acid sequence of the murine polypeptide are shown in Figure 2 and in SEQ ID NOs:4 and 5, respectively.
  • the murine BAL gene which is approximately 3024 nucleotides in length, encodes a protein having a molecular weight of approximately 95 kD and which is approximately 826 amino acid residues in length.
  • nucleic acid molecules that encode BAL proteins or biologically active portions thereof, as well as nucleic acid fragments sufficient for use as hybridization probes to identify BAL-encoding nucleic acid molecules (e.g., BAL mRNA) and fragments for use as PCR primers for the amplification or mutation of BAL nucleic acid molecules.
  • BAL mRNA BAL-encoding nucleic acid molecules
  • nucleic acid molecule is intended to include DNA molecules (e.g., cDNA or genomic DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated using nucleotide analogs.
  • the nucleic acid molecule can be single-stranded or double- stranded, but preferably is double-stranded DNA.
  • isolated nucleic acid molecule includes nucleic acid molecules which are separated from other nucleic acid molecules which are present in the natural source of the nucleic acid.
  • isolated includes nucleic acid molecules which are separated from the chromosome with which the genomic DNA is naturally associated.
  • an "isolated" nucleic acid is free of sequences which naturally flank the nucleic acid (i.e., sequences located at the 5' and 3' ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived.
  • the isolated BAL nucleic acid molecule can contain less than about 5 kb, 4kb, 3kb, 2kb, 1 kb, 0.5 kb or OJ kb of nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived.
  • an "isolated" nucleic acid molecule such as a cDNA molecule, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.
  • a nucleic acid molecule of the present invention e.g., a nucleic acid molecule having the nucleotide sequence of SEQ ID NO: 1, 3, 4, or 6 or a portion thereof, can be isolated using standard molecular biology techniques and the sequence information provided herein. Using all or portion of the nucleic acid sequence of SEQ ID NOJ, 3, 4, or 6, as a hybridization probe, BAL nucleic acid molecules can be isolated using standard hybridization and cloning techniques (e.g., as described in Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989).
  • nucleic acid molecule encompassing all or a portion of SEQ ID NOJ, 3, 4, or 6 can be isolated by the polymerase chain reaction (PCR) using synthetic oligonucleotide primers designed based upon the sequence of SEQ ID NOJ, 3, 4, or 6.
  • a nucleic acid of the invention can be amplified using cDNA, mRNA or alternatively, genomic DNA, as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques. The nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis.
  • an isolated nucleic acid molecule of the invention comprises the nucleotide sequence shown in SEQ ID NO: 1.
  • the sequence of SEQ ID NO: 1 corresponds to the human BAL cDNA.
  • This cDNA comprises sequences encoding the human BAL protein (i.e., "the coding region", from nucleotides 229-2790), as well as 5' untranslated sequences (nucleotides 1-228) and 3' untranslated sequences (nucleotides 2791-3243).
  • the nucleic acid molecule can comprise only the coding region of SEQ ID NO:l (e.g., nucleotides 229-2790, corresponding to SEQ ID NOJ).
  • an isolated nucleic acid molecule of the invention comprises the nucleotide sequence shown in SEQ ID NO:4.
  • the sequence of SEQ ID NO:4 corresponds to the murine BAL cDNA.
  • This cDNA comprises sequences encoding the murine BAL protein (i.e., "the coding region", from nucleotides 171-2648), as well as 5' untranslated sequences (nucleotides 1-170) and 3' untranslated sequences (nucleotides 2649-3024).
  • the nucleic acid molecule can comprise only the coding region of SEQ ID NO:4 (e.g., nucleotides 171-2648, corresponding to SEQ ID NO:6).
  • an isolated nucleic acid molecule of the invention comprises a nucleic acid molecule which is a complement of the nucleotide sequence shown in SEQ ID NOJ, 3, 4, or 6, or a portion of any of these nucleotide sequences.
  • a nucleic acid molecule which is complementary to the nucleotide sequence shown in SEQ ID NO: 1 , 3, 4, or 6, is one which is sufficiently complementary to the nucleotide sequence shown in SEQ ID NOJ, 3, 4, or 6, such that it can hybridize to the nucleotide sequence shown in SEQ ID NOJ, 3, 4, or 6.
  • an isolated nucleic acid molecule of the present invention comprises a nucleotide sequence which is at least about 50%, 55%, 60%, 65%, 70%, 72%, 75%, 80%, 85%, 90%, 95%, 98% or more homologous to the entire length of the nucleotide sequence shown in SEQ ID NOJ, 3, 4, or 6 or a portion of any of these nucleotide sequences.
  • the nucleic acid molecule of the invention can comprise only a portion of the nucleic acid sequence of SEQ ID NOJ, 3, 4, or 6, for example, a fragment which can be used as a probe or primer or a fragment encoding a portion of a BAL protein, e.g. , a biologically active portion of a BAL protein.
  • the nucleotide sequence determined from the cloning of the BAL gene allows for the generation of probes and primers designed for use in identifying and/or cloning other BAL family members, as well as BAL homologues from other species.
  • the probe/primer typically comprises substantially purified oligonucleotide.
  • the oligonucleotide typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12 or 15, preferably about 20 or 25, more preferably about 30, 35, 40, 45, 50, 55, 60, 65, or 75 consecutive nucleotides of a sense sequence of SEQ ID NOJ, 3, 4, or 6, of an anti-sense sequence of SEQ ID NO: 1 , 3, 4, or 6, or of a naturally occurring allelic variant or mutant of SEQ ID NO: 1 , 3, 4, or 6.
  • a nucleic acid molecule of the present invention comprises a nucleotide sequence which is greater than 300-350, 350-400, 400-450, 452, 452-500, 500-550, 550-600, 607, 607-650, 650-700, 700-750, 750-800, 800-850, 850-900, 900-950, 950-1000, or more nucleotides in length and hybridizes under stringent hybridization conditions to a nucleic acid molecule of SEQ ID NOJ, 3, 4, or 6.
  • Probes based on the BAL nucleotide sequences can be used to detect transcripts or genomic sequences encoding the same or homologous proteins.
  • the probe further comprises a label group attached thereto, e.g., the label group can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme co- factor.
  • Such probes can be used as a part of a diagnostic test kit for identifying cells or tissue which misexpress a BAL protein, such as by measuring a level of a BAL- encoding nucleic acid in a sample of cells from a subject e.g., detecting BAL mRNA levels or determining whether a genomic BAL gene has been mutated or deleted.
  • a nucleic acid fragment encoding a "biologically active portion of a BAL protein” can be prepared by isolating a portion of the nucleotide sequence of SEQ ID NO: 1 , 3, 4, or 6, which encodes a polypeptide having a BAL biological activity (the biological activities of the BAL proteins are described herein), expressing the encoded portion of the BAL protein (e.g., by recombinant expression in vitro) and assessing the activity of the encoded portion of the BAL protein.
  • the invention further encompasses nucleic acid molecules that differ from the nucleotide sequence shown in SEQ ID NOJ, 3, 4, or 6, due to degeneracy of the genetic code and thus encode the same BAL proteins as those encoded by the nucleotide sequence shown in SEQ ID NOJ, 3, 4, or 6.
  • an isolated nucleic acid molecule of the invention has a nucleotide sequence encoding a protein having an amino acid sequence shown in SEQ ID NOJ or 5.
  • DNA sequence polymorphisms that lead to changes in the amino acid sequences of the BAL proteins may exist within a population (e.g., the human population). Such genetic polymorphism in the BAL genes may exist among individuals within a population due to natural allelic variation.
  • the terms "gene” and “recombinant gene” refer to nucleic acid molecules which include an open reading frame encoding a BAL protein, preferably a mammalian BAL protein, and can further include non-coding regulatory sequences, and introns.
  • Allelic variants of human BAL include both functional and non-functional BAL proteins.
  • Functional allelic variants are naturally occurring amino acid sequence variants of the human BAL protein that maintain the ability to bind a BAL ligand and/or modulate the occurrence or severity of a malignancy such as a lymphoma, e.g., non- Hodgkin's lymphoma.
  • Functional allelic variants will typically contain only conservative substitution of one or more amino acids of SEQ ID NOJ or 5 or substitution, deletion or insertion of non-critical residues in non-critical regions of the protein.
  • Non-functional allelic variants are naturally occurring amino acid sequence variants of the human BAL protein that do not have the ability to either bind a BAL ligand and/or modulate occurrence or severity of a malignancy such as a lymphoma, e.g., non-Hodgkin's lymphoma.
  • Non-functional allelic variants will typically contain a non-conservative substitution, a deletion, or insertion or premature truncation of the amino acid sequence of SEQ ID NOJ or 5 or a substitution, insertion or deletion in critical residues or critical regions.
  • the present invention further provides non-human orthologues of the human BAL protein.
  • Orthologues of the human BAL protein are proteins that are isolated from non-human organisms and possess the same BAL ligand binding and/or modulation of the occurrence or severity of a malignancy such as a lymphoma, e.g., non-Hodgkin's lymphoma capabilities of the human BAL protein.
  • Orthologues of the human BAL protein can readily be identified as comprising an amino acid sequence that is substantially homologous to SEQ ID NOJ or 5.
  • nucleic acid molecules encoding other BAL family members and, thus, which have a nucleotide sequence which differs from the BAL sequences of SEQ ID NO:l, 3, 4, or 6 are intended to be within the scope of the invention.
  • another BAL cDNA can be identified based on the nucleotide sequence of human BAL.
  • nucleic acid molecules encoding BAL proteins from different species, and which, thus, have a nucleotide sequence which differs from the BAL sequences of SEQ ID NOJ, 3, 4, or 6 are intended to be within the scope of the invention.
  • a monkey BAL cDNA can be identified based on the nucleotide sequence of a human or murine BAL.
  • Nucleic acid molecules corresponding to natural allelic variants and homologues of the BAL cDNAs of the invention can be isolated based on their homology to the BAL nucleic acids disclosed herein using the cDNAs disclosed herein, or a portion thereof, as a hybridization probe according to standard hybridization techniques under stringent hybridization conditions. Nucleic acid molecules corresponding to natural allelic variants and homologues of the BAL cDNAs of the invention can further be isolated by mapping to the same chromosome or locus as the BAL gene.
  • an isolated nucleic acid molecule of the invention is at least 15, 20, 25, 30 or more nucleotides in length and hybridizes under stringent conditions to the nucleic acid molecule comprising the nucleotide sequence of SEQ ID NOJ, 3, 4, or 6.
  • the nucleic acid is at least 30, 50, 100, 150, 200, 250, 300, 350, 400, 450, 452, 500, 550, 607, 600, 650, 700, 750, 800, 850, 900, or 950 nucleotides in length.
  • hybridizes under stringent conditions is intended to describe conditions for hybridization and washing under which nucleotide sequences at least 60% homologous to each other typically remain hybridized to each other.
  • the conditions are such that sequences at least about 70%, more preferably at least about 80%, even more preferably at least about 85% or 90%) homologous to each other typically remain hybridized to each other.
  • stringent conditions are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6.
  • a preferred, non-limiting example of stringent hybridization conditions are hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45°C, followed by one or more washes in 0.2 X SSC, 0.1% SDS at 50°C, preferably at 55°C, more preferably at 60°C, and even more preferably at 65°C.
  • SSC sodium chloride/sodium citrate
  • an isolated nucleic acid molecule of the invention that hybridizes under stringent conditions to the sequence of SEQ ID NO:l, 3, 4, or 6 corresponds to a naturally-occurring nucleic acid molecule.
  • a "naturally-occurring" nucleic acid molecule refers to an RNA or DNA molecule having a nucleotide sequence that occurs in nature (e.g., encodes a natural protein).
  • allelic variants of the BAL sequences that may exist in the population, the skilled artisan will further appreciate that changes can be introduced by mutation into the nucleotide sequences of SEQ ID NO:l, 3, 4, or 6 thereby leading to changes in the amino acid sequence of the encoded BAL proteins, without altering the functional ability of the BAL proteins.
  • nucleotide substitutions leading to amino acid substitutions at "non-essential" amino acid residues can be made in the sequence of SEQ ID NO:l, 3, 4, or 6.
  • non-essential amino acid residue is a residue that can be altered from the wild-type sequence of BAL (e.g., the sequence of SEQ ID NO:2 or 5) without altering the biological activity, whereas an "essential" amino acid residue is required for biological activity.
  • amino acid residues that are conserved among the BAL proteins of the present invention are predicted to be particularly unamenable to alteration.
  • additional amino acid residues that are conserved between the BAL proteins of the present invention and other members of the BAL family are not likely to be amenable to alteration.
  • nucleic acid molecules encoding BAL proteins that contain changes in amino acid residues that are not essential for activity. Such BAL proteins differ in amino acid sequence from SEQ ID NOJ or 5, yet retain biological activity.
  • the isolated nucleic acid molecule comprises a nucleotide sequence encoding a protein, wherein the protein comprises an amino acid sequence at least about 50%, 55%, 60%, 62%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% or more homologous to SEQ ID NOJ or 5.
  • An isolated nucleic acid molecule encoding a BAL protein homologous to the protein of SEQ ID NOJ or 5 can be created by introducing one or more nucleotide substitutions, additions or deletions into the nucleotide sequence of SEQ ID NO: 1, 3, 4, or 6, such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein. Mutations can be introduced into SEQ ID NOJ, 3, 4, or 6, by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Preferably, conservative amino acid substitutions are made at one or more predicted non- essential amino acid residues. A "conservative amino acid substitution" is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain.
  • Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine).
  • basic side chains e.g., lysine, arginine, histidine
  • acidic side chains e.g.
  • a predicted nonessential amino acid residue in a BAL protein is preferably replaced with another amino acid residue from the same side chain family.
  • mutations can be introduced randomly along all or part of a BAL coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for BAL biological activity to identify mutants that retain activity. Following mutagenesis of SEQ ID NOJ, 3, 4, or 6, the encoded protein can be expressed recombinantly and the activity of the protein can be determined. In a preferred embodiment, a mutant BAL protein can be assayed for the ability to
  • a non-BAL protein molecule e.g., CRK, CRK-L, SHP-2, PBK, or ZAP70
  • a BAL-dependent signal transduction pathway e.g., CRK, CRK-L, SHP-2, PBK, or ZAP70
  • a lymphoma e.g., non Hodgkin's lymphoma
  • an antisense nucleic acid comprises a nucleotide sequence which is complementary to a "sense" nucleic acid encoding a protein, e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence. Accordingly, an antisense nucleic acid can hydrogen bond to a sense nucleic acid.
  • the antisense nucleic acid can be complementary to an entire BAL coding strand, or to only a portion thereof.
  • an antisense nucleic acid molecule is antisense to a "coding region" of the coding strand of a nucleotide sequence encoding BAL.
  • the term "coding region” refers to the region of the nucleotide sequence comprising codons which are translated into amino acid residues (e.g., the coding region of human and murine BAL corresponds to SEQ ID NOJ and 6, respectively).
  • the antisense nucleic acid molecule is antisense to a "noncoding region" of the coding strand of a nucleotide sequence encoding BAL.
  • noncoding region refers to 5' and 3' sequences which flank the coding region that are not translated into amino acids (i.e., also referred to as 5' and 3' untranslated regions). Given the coding strand sequences encoding BAL disclosed herein (e.g., SEQ ID NO: 1
  • antisense nucleic acids of the invention can be designed according to the rules of Watson and Crick base pairing.
  • the antisense nucleic acid molecule can be complementary to the entire coding region of BAL mRNA, but more preferably is an oligonucleotide which is antisense to only a portion of the coding or noncoding region of BAL mRNA.
  • the antisense oligonucleotide can be complementary to the region surrounding the translation start site of BAL mRNA.
  • An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length.
  • an antisense nucleic acid of the invention can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art.
  • an antisense nucleic acid e.g., an antisense oligonucleotide
  • an antisense nucleic acid can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids, e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used.
  • modified nucleotides which can be used to generate the antisense nucleic acid include 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xantine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5- carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1- methylguanine, 1 -methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2- methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5- methylaminomethyluracil, 5-methoxyaminornefhyl-2-thiouracil, beta-D- mannosylqueosine,
  • the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection).
  • the antisense nucleic acid molecules of the invention are typically administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a BAL protein to thereby inhibit expression of the protein, e.g. , by inhibiting transcription and/or translation.
  • the hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule which binds to DNA duplexes, through specific interactions in the major groove of the double helix.
  • An example of a route of administration of antisense nucleic acid molecules of the invention include direct injection at a tissue site.
  • antisense nucleic acid molecules can be modified to target selected cells and then administered systemically.
  • antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecules to peptides or antibodies which bind to cell surface receptors or antigens.
  • the antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations of the antisense molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter are preferred.
  • the antisense nucleic acid molecule of the invention is an ⁇ -anomeric nucleic acid molecule.
  • An ⁇ -anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual ⁇ -units, the strands run parallel to each other (Gaultier et al. (1987) Nucleic Acids. Res. 15:6625-6641).
  • the antisense nucleic acid molecule can also comprise a 2'-o- methylribonucleotide (Inoue et al. (1987) Nucleic Acids Res. 15:6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett. 215:327-330).
  • an antisense nucleic acid of the invention is a ribozyme.
  • Ribozymes are catalytic RNA molecules with ribonuclease activity which are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region.
  • ribozymes e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334:585-591)) can be used to catalytically cleave BAL mRNA transcripts to thereby inhibit translation of BAL mRNA.
  • a ribozyme having specificity for a BAL-encoding nucleic acid can be designed based upon the nucleotide sequence of a BAL cDNA disclosed herein (i.e., SEQ ID NOJ, 3, 4, or 6).
  • a derivative of a Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in a BAL-encoding mRNA. See, e.g., Cech et al. U.S. Patent No. 4,987,071; and Cech et al. U.S. Patent No. 5,116,742.
  • BAL mRNA can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel, D. and Szostak, J.W. (1993) Science 261 :1411-1418.
  • BAL gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region of the BAL (e.g., the BAL promoter and/or enhancers) to form triple helical structures that prevent transcription of the BAL gene in target cells.
  • nucleotide sequences complementary to the regulatory region of the BAL e.g., the BAL promoter and/or enhancers
  • BAL promoter and/or enhancers e.g., the BAL promoter and/or enhancers
  • the BAL nucleic acid molecules of the present invention can be modified at the base moiety, sugar moiety or phosphate backbone to improve, e.g., the stability, hybridization, or solubility of the molecule.
  • the deoxyribose phosphate backbone of the nucleic acid molecules can be modified to generate peptide nucleic acids (see Hyrup B. et al. (1996) Bioorganic & Medicinal Chemistry 4 (1): 5-23).
  • peptide nucleic acids refer to nucleic acid mimics, e.g., DNA mimics, in which the deoxyribose phosphate backbone is replaced by a pseudopeptide backbone and only the four natural nucleobases are retained.
  • the neutral backbone of PNAs has been shown to allow for specific hybridization to DNA and RNA under conditions of low ionic strength.
  • the synthesis of PNA oligomers can be performed using standard solid phase peptide synthesis protocols as described in Hyrup B. et al. (1996) supra; Perry-O'Keefe et al. Proc. Natl. Acad. Sci. 93: 14670-675.
  • PNAs of BAL nucleic acid molecules can be used in therapeutic and diagnostic applications.
  • PNAs can be used as antisense or antigene agents for sequence-specific modulation of gene expression by, for example, inducing transcription or translation arrest or inhibiting replication.
  • PNAs of BAL nucleic acid molecules can also be used in the analysis of single base pair mutations in a gene, (e.g., by PNA- directed PCR clamping); as 'artificial restriction enzymes' when used in combination with other enzymes, (e.g., SI nucleases (Hyrup B. (1996) supra)); or as probes or primers for DNA sequencing or hybridization (Hyrup B. et al. (1996) supra; Perry- O'Keefe supra).
  • PNAs of BAL can be modified, (e.g., to enhance their stability or cellular uptake), by attaching lipophilic or other helper groups to PNA, by the formation of PNA-DNA chimeras, or by the use of liposomes or other techniques of drug delivery known in the art.
  • PNA-DNA chimeras of BAL nucleic acid molecules can be generated which may combine the advantageous properties of PNA and DNA.
  • Such chimeras allow DNA recognition enzymes, (e.g. , RNAse H and DNA polymerases), to interact with the DNA portion while the PNA portion would provide high binding affinity and specificity.
  • PNA-DNA chimeras can be linked using linkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleobases, and orientation (Hyrup B. (1996) supra).
  • the synthesis of PNA-DNA chimeras can be performed as described in Hyrup B. (1996) supra and Finn P.J. et al. (1996) Nucleic Acids Res. 24 (17): 3357-63.
  • a DNA chain can be synthesized on a solid support using standard phosphoramidite coupling chemistry and modified nucleoside analogs, e.g., 5'-(4-methoxytrityl)amino-5'-deoxy-thymidine phosphoramidite, can be used as a between the PNA and the 5' end of DNA (Mag, M. et al. (1989) Nucleic Acid Res. 17: 5973-88). PNA monomers are then coupled in a stepwise manner to produce a chimeric molecule with a 5' PNA segment and a 3' DNA segment (Finn P.J. et al. (1996) supra).
  • modified nucleoside analogs e.g., 5'-(4-methoxytrityl)amino-5'-deoxy-thymidine phosphoramidite
  • chimeric molecules can be synthesized with a 5' DNA segment and a 3' PNA segment (Peterser, K.H. et al. (1975) Bioorganic Med. Chem. Lett. 5 : 1119- 11124).
  • the oligonucleotide may include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger et al. (1989) Proc. Natl. Acad. Sci. USA 86:6553-6556; Lemaitre et al. (1987) Proc. Natl. Acad. Sci. USA 84:648-652; PCT Publication No. W088/09810) or the blood-brain barrier (see, e.g. , PCT Publication No. W089/10134).
  • peptides e.g., for targeting host cell receptors in vivo
  • agents facilitating transport across the cell membrane see, e.g., Letsinger et al. (1989) Proc. Natl. Acad. Sci. USA 86:6553-6556; Lemaitre et al. (1987) Proc. Natl. Ac
  • oligonucleotides can be modified with hybridization- triggered cleavage agents (See, e.g., Krol et al. (1988) Bio-Techniques 6:958-976) or intercalating agents. (See, e.g., Zon (1988) Pharm. Res. 5:539-549).
  • the oligonucleotide may be conjugated to another molecule, (e.g., a peptide, hybridization triggered cross-linking agent, transport agent, or hybridization-triggered cleavage agent).
  • BAL proteins can be isolated from cells or tissue sources by an appropriate purification scheme using standard protein purification techniques.
  • BAL proteins are produced by recombinant DNA techniques.
  • a BAL protein or polypeptide can be synthesized chemically using standard peptide synthesis techniques.
  • An "isolated” or “purified” protein or biologically active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the BAL protein is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized.
  • the language “substantially free of cellular material” includes preparations of BAL protein in which the protein is separated from cellular components of the cells from which it is isolated or recombinantly produced.
  • the language “substantially free of cellular material” includes preparations of BAL protein having less than about 30% (by dry weight) of non-BAL protein (also referred to herein as a "contaminating protein”), more preferably less than about 20% of non-BAL protein, still more preferably less than about 10% of non-BAL protein, and most preferably less than about 5%> non-BAL protein.
  • the BAL protein or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%), and most preferably less than about 5% of the volume of the protein preparation.
  • the language “substantially free of chemical precursors or other chemicals” includes preparations of BAL protein in which the protein is separated from chemical precursors or other chemicals which are involved in the synthesis of the protein.
  • the language “substantially free of chemical precursors or other chemicals” includes preparations of BAL protein having less than about 30%> (by dry weight) of chemical precursors or non-BAL chemicals, more preferably less than about 20%> chemical precursors or non-BAL chemicals, still more preferably less than about 10% chemical precursors or non-BAL chemicals, and most preferably less than about 5%> chemical precursors or non-BAL chemicals.
  • a "biologically active portion" of a BAL protein includes a fragment of a BAL protein which participates in an interaction between a BAL molecule and a non-BAL molecule.
  • Biologically active portions of a BAL protein include peptides comprising amino acid sequences sufficiently homologous to or derived from the amino acid sequence of the BAL protein, e.g., the amino acid sequence shown in SEQ ID NOJ or 5, which include less amino acids than the full length BAL proteins, and exhibit at least one activity of a BAL protein.
  • biologically active portions comprise a domain or motif with at least one activity of the BAL protein, e.g. , modulating cellular adhesion.
  • a biologically active portion of a BAL protein can be a polypeptide which is, for example, 10, 25, 50, 100, 200 or more amino acids in length.
  • Biologically active portions of a BAL protein can be used as targets for developing agents which modulate a BAL mediated activity, e.g., the occurrence or severity of a lymphoma, e.g., non-Hodgkin's lymphoma.
  • a biologically active portion of a BAL protein comprises at least one proline rich domain and/or at least one tyrosine phosphorylation site. It is to be understood that a preferred biologically active portion of a BAL protein of the present invention may contain at least one of the above-identified structural domains. A more preferred biologically active portion of a BAL protein may contain at least two of the above-identified structural domains. Moreover, other biologically active portions, in which other regions of the protein are deleted, can be prepared by recombinant techniques and evaluated for one or more of the functional activities of a native BAL protein. In a preferred embodiment, the BAL protein has an amino acid sequence shown in SEQ ID NOJ or 5.
  • the BAL protein is substantially homologous to SEQ ID NOJ or 5, and retains the functional activity of the protein of SEQ ID NOJ or 5, yet differs in amino acid sequence due to natural allelic variation or mutagenesis, as described in detail in subsection I above. Accordingly, in another embodiment, the BAL protein is a protein which comprises an amino acid sequence at least about 50%, 55%, 60%, 62%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98% or more homologous to SEQ ID NOJ or 5.
  • sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes).
  • the length of a reference sequence aligned for comparison purposes is at least 30%, preferably at least 40%, more preferably at least 50%, even more preferably at least 60%, and even more preferably at least 70%, 80%, or 90% of the length of the reference sequence (e.g., when aligning a second sequence to the BAL amino acid sequence of SEQ ID NOJ or 5 having 177 amino acid residues, at least 80, preferably at least 100, more preferably at least 120, even more preferably at least 140, and even more preferably at least 150, 160 or 170 amino acid residues are aligned).
  • the amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared.
  • amino acid or nucleic acid “identity” is equivalent to amino acid or nucleic acid "homology”).
  • the percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
  • the comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
  • the percent identity between two amino acid sequences is determined using the Needleman and Wunsch (J. Mol. Biol. (48):444-453 (1970)) algorithm which has been incorporated into the GAP program in the GCG software package (available at http://www.gcg.com), using either a Blosum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6.
  • the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package (available at http://www.gcg.com), using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6.
  • the percent identity between two amino acid or nucleotide sequences is determined using the algorithm of E. Meyers and W. Miller (CABIOS, 4:11-17 (1989)) which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.
  • the nucleic acid and protein sequences of the present invention can further be used as a "query sequence" to perform a search against public databases to, for example, identify other family members or related sequences.
  • Such searches can be performed using the NBLAST and XBLAST programs (version 2.0) of Altschul, et al. (1990) J. Mol. Biol. 215:403-10.
  • Gapped BLAST can be utilized as described in Altschul et al, (1997) Nucleic Acids Res. 25(17):3389-3402.
  • the default parameters of the respective programs e.g., XBLAST and NBLAST
  • the invention also provides BAL chimeric or fusion proteins. As used herein, a
  • BAL "chimeric protein” or “fusion protein” comprises a BAL polypeptide operatively linked to a non-BAL polypeptide.
  • An "BAL polypeptide” refers to a polypeptide having an amino acid sequence corresponding to BAL
  • a non-BAL polypeptide refers to a polypeptide having an amino acid sequence corresponding to a protein which is not substantially homologous to the BAL protein, e.g. , a protein which is different from the BAL protein and which is derived from the same or a different organism.
  • the BAL polypeptide can correspond to all or a portion of a BAL protein.
  • a BAL fusion protein comprises at least one biologically active portion of a BAL protein. In another preferred embodiment, a BAL fusion protein comprises at least two biologically active portions of a BAL protein.
  • the term "operatively linked" is intended to indicate that the BAL polypeptide and the non-BAL polypeptide are fused in-frame to each other. The non- BAL polypeptide can be fused to the N-terminus or C-terminus of the BAL polypeptide.
  • the fusion protein is a GST-BAL fusion protein in which the BAL sequences are fused to the C-terminus of the GST sequences.
  • Such fusion proteins can facilitate the purification of recombinant BAL.
  • the fusion protein is a BAL protein containing a heterologous signal sequence at its N-terminus.
  • expression and/or secretion of BAL can be increased through use of a heterologous signal sequence.
  • the BAL fusion proteins of the invention can be incorporated into pharmaceutical compositions and administered to a subject in vivo.
  • the BAL fusion proteins can be used to affect the bioavailability of a BAL substrate.
  • BAL fusion proteins may be useful therapeutically for the treatment of disorders caused by, for example, (i) aberrant modification or mutation of a gene encoding a BAL protein; (ii) mis-regulation of the BAL gene; and (iii) aberrant post-translational modification of a BAL protein.
  • the BAL-fusion proteins of the invention can be used as immunogens to produce anti-BAL antibodies in a subject, to purify BAL ligands and in screening assays to identify molecules which inhibit the interaction of BAL with a BAL substrate.
  • a BAL chimeric or fusion protein of the invention is produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, for example by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation.
  • the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers.
  • PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and reamplified to generate a chimeric gene sequence (see, for example, Current Protocols in Molecular Biology, eds. Ausubel et al. John Wiley & Sons: 1992).
  • many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide).
  • An BAL- encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the BAL protein.
  • the present invention also pertains to variants of the BAL proteins which function as either BAL agonists (mimetics) or as BAL antagonists. Variants of the BAL proteins can be generated by mutagenesis, e.g., discrete point mutation or truncation of a BAL protein. An agonist of the BAL proteins can retain substantially the same, or a subset, of the biological activities of the naturally occurring form of a BAL protein.
  • An antagonist of a BAL protein can inhibit one or more of the activities of the naturally occurring form of the BAL protein by, for example, competitively modulating a BAL- mediated activity of a BAL protein.
  • specific biological effects can be elicited by treatment with a variant of limited function.
  • treatment of a subject with a variant having a subset of the biological activities of the naturally occurring form of the protein has fewer side effects in a subject relative to treatment with the naturally occurring form of the BAL protein.
  • variants of a BAL protein which function as either BAL agonists (mimetics) or as BAL antagonists can be identified by screening combinatorial libraries of mutants, e.g., truncation mutants, of a BAL protein for BAL protein agonist or antagonist activity.
  • a variegated library of BAL variants is generated by combinatorial mutagenesis at the nucleic acid level and is encoded by a variegated gene library.
  • a variegated library of BAL variants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into gene sequences such that a degenerate set of potential BAL sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g. , for phage display) containing the set of BAL sequences therein.
  • a degenerate set of potential BAL sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g. , for phage display) containing the set of BAL sequences therein.
  • fusion proteins e.g. , for phage display
  • degenerate set of genes allows for the provision, in one mixture, of all of the sequences encoding the desired set of potential BAL sequences.
  • Methods for synthesizing degenerate oligonucleotides are known in the art (see, e.g., Narang, S.A. (1983) Tetrahedron 39:3; Itakura et al. (1984) Annu. Rev. Biochem. 53:323; Itakura et al. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res. 11 :477.
  • libraries of fragments of a BAL protein coding sequence can be used to generate a variegated population of BAL fragments for screening and subsequent selection of variants of a BAL protein.
  • a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of a BAL coding sequence with a nuclease under conditions wherein nicking occurs only about once per molecule, denaturing the double stranded DNA, renaturing the DNA to form double stranded DNA which can include sense/antisense pairs from different nicked products, removing single stranded portions from reformed duplexes by treatment with S 1 nuclease, and ligating the resulting fragment library into an expression vector.
  • an expression library can be derived which encodes N-terminal, C-terminal and internal fragments of various sizes of the BAL protein.
  • Recrusive ensemble mutagenesis (REM), a new technique which enhances the frequency of functional mutants in the libraries, can be used in combination with the screening assays to identify BAL variants (Arkin and Yourvan (1992) Proc. Natl. Acad. Sci. USA 59:7811-7815; Delgrave et al. (1993) Protein Engineering 6(3):327-331).
  • cell based assays can be exploited to analyze a variegated BAL library. For example, a library of expression vectors can be transfected into a cell line which ordinarily responds to a particular ligand in a BAL-dependent manner.
  • the transfected cells are then contacted with the ligand and the effect of expression of the mutant on signaling by the ligand can be detected, e.g., by measuring cell survival or the activity of a BAL-regulated transcription factor. Plasmid DNA can then be recovered from the cells which score for inhibition, or alternatively, potentiation of signaling by the ligand, and the individual clones further characterized.
  • An isolated BAL protein, or a portion or fragment thereof, can be used as an immunogen to generate antibodies that bind BAL using standard techniques for polyclonal and monoclonal antibody preparation.
  • a full-length BAL protein can be used or, alternatively, the invention provides antigenic peptide fragments of BAL for use as immunogens.
  • the antigenic peptide of BAL comprises at least 8 amino acid residues of the amino acid sequence shown in SEQ ID NOJ or 5 and encompasses an epitope of BAL such that an antibody raised against the peptide forms a specific immune complex with BAL.
  • the antigenic peptide comprises at least 10 amino acid residues, more preferably at least 15 amino acid residues, even more preferably at least 20 amino acid residues, and most preferably at least 30 amino acid residues.
  • Preferred epitopes encompassed by the antigenic peptide are regions of BAL that are located on the surface of the protein, e.g., hydrophilic regions, as well as regions with high antigenicity.
  • a BAL immunogen typically is used to prepare antibodies by immunizing a suitable subject, (e.g., rabbit, goat, mouse or other mammal) with the immunogen.
  • An appropriate immunogenic preparation can contain, for example, recombinantly expressed BAL protein or a chemically synthesized BAL polypeptide.
  • the preparation can further include an adjuvant, such as Freund's complete or incomplete adjuvant, or similar immuno stimulatory agent. Immunization of a suitable subject with an immunogenic BAL preparation induces a polyclonal anti-BAL antibody response.
  • antibody refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i. e. , molecules that contain an antigen binding site which specifically binds (immunoreacts with) an antigen, such as BAL.
  • immunologically active portions of immunoglobulin molecules include F(ab) and F(ab') 2 fragments which can be generated by treating the antibody with an enzyme such as pepsin.
  • the invention provides polyclonal and monoclonal antibodies that bind BAL.
  • monoclonal antibody or “monoclonal antibody composition”, as used herein, refers to a population of antibody molecules that contain only one species of an antigen binding site capable of immunoreacting with a particular epitope of BAL.
  • a monoclonal antibody composition thus typically displays a single binding affinity for a particular BAL protein with which it immunoreacts.
  • Polyclonal anti-BAL antibodies can be prepared as described above by immunizing a suitable subject with a BAL immunogen.
  • the anti-BAL antibody titer in the immunized subject can be monitored over time by standard techniques, such as with an enzyme linked immunosorbent assay (ELISA) using immobilized BAL.
  • ELISA enzyme linked immunosorbent assay
  • the antibody molecules directed against BAL can be isolated from the mammal (e.g., from the blood) and further purified by well known techniques, such as protein A chromatography to obtain the IgG fraction.
  • antibody-producing cells can be obtained from the subject and used to prepare monoclonal antibodies by standard techniques, such as the hybridoma technique originally described by Kohler and Milstein (1975) Nature 256:495-497) (see also, Brown et al. (1981) J. Immunol. 127:539-46; Brown et al. (1980) J. Biol. Chem .255:4980-83; Yeh et al. (1976) Proc. Natl. Acad. Sci. USA 76:2927-31; and Yeh et al. (1982) Int. J.
  • an immortal cell line typically a myeloma
  • lymphocytes typically splenocytes
  • lymphocytes typically splenocytes
  • Any of the many well known protocols used for fusing lymphocytes and immortalized cell lines can be applied for the purpose of generating an anti-BAL monoclonal antibody (see, e.g., G. Galfre et al. (1977) Nature 266:55052; Gefter et al.
  • the immortal cell line e.g., a myeloma cell line
  • murine hybridomas can be made by fusing lymphocytes from a mouse immunized with an immunogenic preparation of the present invention with an immortalized mouse cell line.
  • Preferred immortal cell lines are mouse myeloma cell lines that are sensitive to culture medium containing hypoxanthine, aminopterin and thymidine ("HAT medium"). Any of a number of myeloma cell lines can be used as a fusion partner according to standard techniques, e.g., the P3-NSl/l-Ag4-l, P3-x63-Ag8.653 or Sp2/O-Agl4 myeloma lines. These myeloma lines are available from ATCC. Typically, HAT-sensitive mouse myeloma cells are fused to mouse splenocytes using polyethylene glycol (“PEG").
  • PEG polyethylene glycol
  • Hybridoma cells resulting from the fusion are then selected using HAT medium, which kills unfused and unproductively fused myeloma cells (unfused splenocytes die after several days because they are not transformed).
  • Hybridoma cells producing a monoclonal antibody of the invention are detected by screening the hybridoma culture supernatants for antibodies that bind BAL, e.g., using a standard ELISA assay.
  • a monoclonal anti-BAL antibody can be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g., an antibody phage display library) with BAL to thereby isolate immunoglobulin library members that bind BAL.
  • Kits for generating and screening phage display libraries are commercially available (e.g., the Pharmacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; and the Stratagene SurfZAPTM Phage Display Kit, Catalog No. 240612).
  • examples of methods and reagents particularly amenable for use in generating and screening antibody display library can be found in, for example, Ladner et al. U.S.
  • recombinant anti-BAL antibodies such as chimeric and humanized monoclonal antibodies, comprising both human and non-human portions, which can be made using standard recombinant DNA techniques, are within the scope of the invention.
  • Such chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art, for example using methods described in Robinson et al. International Application No. PCT/US86/02269; Akira, et al. European Patent Application 184,187; Taniguchi, M., European Patent Application 171,496; Morrison et al. European Patent Application 173,494; Neuberger et al. PCT
  • An anti-BAL antibody e.g., monoclonal antibody
  • An anti-BAL antibody can be used to isolate BAL by standard techniques, such as affinity chromatography or immunoprecipitation.
  • An anti-BAL antibody can facilitate the purification of natural BAL from cells and of recombinantly produced BAL expressed in host cells.
  • an anti-BAL antibody can be used to detect BAL protein (e.g., in a cellular lysate or cell supernatant) in order to evaluate the abundance and pattern of expression of the BAL protein.
  • Anti-BAL antibodies can be used diagnostically to monitor protein levels in tissue as part of a clinical testing procedure, e.g., to, for example, determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling (/. e. , physically linking) the antibody to a detectable substance.
  • detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials.
  • suitable enzymes include horseradish peroxidase, alkaline phosphatase, -galactosidase, or acetylcholinesterase;
  • suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin;
  • suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin;
  • an example of a luminescent material includes luminol;
  • examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include 125 I, 131 I, 35 S or 3 H.
  • vectors preferably expression vectors, containing a nucleic acid encoding a BAL protein (or a portion thereof).
  • vector refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked.
  • plasmid refers to a circular double stranded DNA loop into which additional DNA segments can be ligated.
  • viral vector Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome.
  • Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g. , bacterial vectors having a bacterial origin of replication and episomal mammalian vectors).
  • vectors e.g., non-episomal mammalian vectors
  • Other vectors are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome.
  • certain vectors are capable of directing the expression of genes to which they are operatively linked.
  • Such vectors are referred to herein as "expression vectors".
  • expression vectors of utility in recombinant DNA techniques are often in the form of plasmids.
  • plasmid and vector can be used interchangeably as the plasmid is the most commonly used form of vector.
  • the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno- associated viruses), which serve equivalent functions.
  • the recombinant expression vectors of the invention comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic acid sequence to be expressed.
  • "operably linked" is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell).
  • regulatory sequence is intended to include promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel; Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990). Regulatory sequences include those which direct constitutive expression of a nucleotide sequence in many types of host cells and those which direct expression of the nucleotide sequence only in certain host cells (e.g., tissue-specific regulatory sequences). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, and the like.
  • the expression vectors of the invention can be introduced into host cells to thereby produce proteins or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein (e.g., BAL proteins, mutant forms of BAL proteins, fusion proteins, and the like).
  • the recombinant expression vectors of the invention can be designed for expression of BAL proteins in prokaryotic or eukaryotic cells.
  • BAL proteins can be expressed in bacterial cells such as E coli, insect cells (using baculovirus expression vectors) yeast cells or mammalian cells. Suitable host cells are discussed further in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990).
  • the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.
  • Fusion vectors add a number of amino acids to a protein encoded therein, usually to the amino terminus of the recombinant protein.
  • Such fusion vectors typically serve three purposes: 1) to increase expression of recombinant protein; 2) to increase the solubility of the recombinant protein; and 3) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification.
  • a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein.
  • enzymes, and their cognate recognition sequences include Factor Xa, thrombin and enterokinase.
  • Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D.B. and Johnson, K.S.
  • fusion proteins can be utilized in BAL activity assays, (e.g., direct assays or competitive assays described in detail below), or to generate antibodies specific for BAL proteins, for example.
  • BAL activity assays e.g., direct assays or competitive assays described in detail below
  • a BAL fusion protein expressed in a retroviral expression vector of the present invention can be utilized to infect bone marrow cells which are subsequently transplanted into irradiated recipients. The pathology of the subject recipient is then examined after sufficient time has passed (e.g., six (6) weeks).
  • Suitable inducible non-fusion E. coli expression vectors include pTrc (Amann et al., (1988) Gene 69:301-315) and pET 1 Id (Studier et al., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California (1990) 60-89).
  • Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid trp-lac fusion promoter.
  • Target gene expression from the pET 1 Id vector relies on transcription from a T7 gnlO-lac fusion promoter mediated by a coexpressed viral RNA polymerase (T7 gnl). This viral polymerase is supplied by host strains BL21 (DE3) or HMS 174(DE3) from a resident prophage harboring a T7 gnl gene under the transcriptional control of the lacUV 5 promoter.
  • nucleic acid sequence of the nucleic acid is altered into an expression vector so that the individual codons for each amino acid are those preferentially utilized in E. coli (Wada et al., (1992) Nucleic Acids Res. 20:2111-2118). Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.
  • the BAL expression vector is a yeast expression vector.
  • yeast expression vectors for expression in yeast S cerivisae include pYepSecl (Baldari, et al., (1987) Embo J. 6:229-234), pMFa (Kurjan and Herskowitz, (1982) Cell 30:933- 943), pJRY88 (Schultz et al., (1987) Gene 54:113-123), pYES2 (Invitrogen Corporation, San Diego, CA), and picZ (InVitrogen Corp, San Diego, CA).
  • BAL proteins can be expressed in insect cells using baculovirus expression vectors.
  • Baculovirus vectors available for expression of proteins in cultured insect cells include the pAc series (Smith et al. (1983) Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklow and Summers (1989) Virology 170:31-39).
  • a nucleic acid of the invention is expressed in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include pCDM8 (Seed, B. (1987) Nature 329:840) and pMT2PC (Kaufman et al. (1987) EMBO J.
  • the expression vector's control functions are often provided by viral regulatory elements.
  • viral regulatory elements For example, commonly used promoters are derived from polyoma, Adenovirus 2, cytomegalovirus and Simian Virus 40.
  • promoters are derived from polyoma, Adenovirus 2, cytomegalovirus and Simian Virus 40.
  • suitable expression systems for both prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989.
  • the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid).
  • tissue-specific regulatory elements are known in the art.
  • suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert et al. (1987) Genes Dev. 1:268-277), lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol. 43:235-275), in particular promoters of T cell receptors (Winoto and Baltimore (1989) EMBO J.
  • promoters are also encompassed, for example the murine hox promoters (Kessel and Gruss (1990) Science 249:374-379) and the ⁇ -fetoprotein promoter (Campes and Tilghman (1989) Genes Dev. 3:537-546).
  • the invention further provides a recombinant expression vector comprising a DNA molecule of the invention cloned into the expression vector in an antisense orientation. That is, the DNA molecule is operatively linked to a regulatory sequence in a manner which allows for expression (by transcription of the DNA molecule) of an RNA molecule which is antisense to BAL mRNA. Regulatory sequences operatively linked to a nucleic acid cloned in the antisense orientation can be chosen which direct the continuous expression of the antisense RNA molecule in a variety of cell types, for instance viral promoters and/or enhancers, or regulatory sequences can be chosen which direct constitutive, tissue specific or cell type specific expression of antisense RNA.
  • the antisense expression vector can be in the form of a recombinant plasmid, phagemid or attenuated virus in which antisense nucleic acids are produced under the control of a high efficiency regulatory region, the activity of which can be determined by the cell type into which the vector is introduced.
  • a high efficiency regulatory region the activity of which can be determined by the cell type into which the vector is introduced.
  • Another aspect of the invention pertains to host cells into which a BAL nucleic acid molecule of the invention is introduced, e.g., a BAL nucleic acid molecule within a recombinant expression vector or a BAL nucleic acid molecule containing sequences which allow it to homologously recombine into a specific site of the host cell's genome.
  • the terms "host cell” and “recombinant host cell” are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.
  • a host cell can be any prokaryotic or eukaryotic cell.
  • a BAL protein can be expressed in bacterial cells such as E. coli, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells).
  • bacterial cells such as E. coli, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells).
  • mammalian cells such as Chinese hamster ovary cells (CHO) or COS cells.
  • Other suitable host cells are known to those skilled in the art.
  • Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques.
  • transformation and “transfection” are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, D ⁇ A ⁇ -dextran-mediated transfection, lipofection, or electroporation. Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al. (Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989), and other laboratory manuals.
  • a gene that encodes a selectable marker (e.g., resistance to antibiotics) is generally introduced into the host cells along with the gene of interest.
  • selectable markers include those which confer resistance to drugs, such as G418, hygromycin and methotrexate.
  • Nucleic acid encoding a selectable marker can be introduced into a host cell on the same vector as that encoding a BAL protein or can be introduced on a separate vector.
  • a host cell of the invention such as a prokaryotic or eukaryotic host cell in culture, can be used to produce (i.e., express) a BAL protein.
  • the invention further provides methods for producing a BAL protein using the host cells of the invention.
  • the method comprises culturing the host cell of invention (into which a recombinant expression vector encoding a BAL protein has been introduced) in a suitable medium such that a BAL protein is produced.
  • the method further comprises isolating a BAL protein from the medium or the host cell.
  • the host cells of the invention can also be used to produce non-human transgenic animals.
  • a host cell of the invention is a fertilized oocyte or an embryonic stem cell into which BAL-coding sequences have been introduced.
  • Such host cells can then be used to create non-human transgenic animals in which exogenous BAL sequences have been introduced into their genome or homologous recombinant animals in which endogenous BAL sequences have been altered.
  • Such animals are useful for studying the function and/or activity of a BAL and for identifying and/or evaluating modulators of BAL activity.
  • a host cell of the invention is a fertilized oocyte or an embryonic stem cell into which BAL-coding sequences have been introduced.
  • Such host cells can then be used to create non-human transgenic animals in which exogenous BAL sequences have been introduced into their genome or homologous recombinant animals in which endogenous BAL sequences have been altered.
  • Such animals are useful for studying the function and/or activity of a BAL and
  • transgenic animal is a non-human animal, preferably a mammal, more preferably a rodent such as a rat or mouse, in which one or more of the cells of the animal includes a transgene.
  • Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, amphibians, and the like.
  • a transgene is exogenous DNA which is integrated into the genome of a cell from which a transgenic animal develops and which remains in the genome of the mature animal, thereby directing the expression of an encoded gene product in one or more cell types or tissues of the transgenic animal.
  • a "homologous recombinant animal” is a non-human animal, preferably a mammal, more preferably a mouse, in which an endogenous BAL gene has been altered by homologous recombination between the endogenous gene and an exogenous DNA molecule introduced into a cell of the animal, e.g., an embryonic cell of the animal, prior to development of the animal.
  • a transgenic animal of the invention can be created by introducing a BAL- encoding nucleic acid into the male pronuclei of a fertilized oocyte, e.g., by microinjection, retro viral infection, and allowing the oocyte to develop in a pseudopregnant female foster animal.
  • the BAL cDNA sequence of SEQ ID NOJ or 4 can be introduced as a transgene into the genome of a non-human animal.
  • a nonhuman homologue of a human BAL gene such as a mouse or rat BAL gene, can be used as a transgene.
  • a BAL gene homologue can be isolated based on hybridization to the BAL cDNA sequences of SEQ ID NOJ, 3, 4, or 6 (described further in subsection I above) and used as a transgene. Intronic sequences and polyadenylation signals can also be included in the transgene to increase the efficiency of expression of the transgene.
  • a tissue-specific regulatory sequence(s) can be operably linked to a BAL transgene to direct expression of a BAL protein to particular cells.
  • transgenic founder animal can be identified based upon the presence of a BAL transgene in its genome and/or expression of BAL mRNA in tissues or cells of the animals. A transgenic founder animal can then be used to breed additional animals carrying the transgene. Moreover, transgenic animals carrying a transgene encoding a BAL protein can further be bred to other transgenic animals carrying other transgenes.
  • a vector which contains at least a portion of a BAL gene into which a deletion, addition or substitution has been introduced to thereby alter, e.g., functionally disrupt, the BAL gene.
  • the BAL gene can be a human gene (e.g., the cDNA of SEQ ID NOJ), but more preferably, is a non- human homologue of a human BAL gene (e.g., the cDNA of SEQ ID NO:6).
  • a mouse BAL gene can be used to construct a homologous recombination nucleic acid molecule, e.g., a vector, suitable for altering an endogenous BAL gene in the mouse genome.
  • the homologous recombination nucleic acid molecule is designed such that, upon homologous recombination, the endogenous BAL gene is functionally disrupted (i.e., no longer encodes a functional protein; also referred to as a "knock out" vector).
  • the homologous recombination nucleic acid molecule can be designed such that, upon homologous recombination, the endogenous BAL gene is mutated or otherwise altered but still encodes functional protein (e.g. , the upstream regulatory region can be altered to thereby alter the expression of the endogenous BAL protein).
  • the altered portion of the BAL gene is flanked at its 5' and 3' ends by additional nucleic acid sequence of the BAL gene to allow for homologous recombination to occur between the exogenous BAL gene carried by the homologous recombination nucleic acid molecule and an endogenous BAL gene in a cell, e.g., an embryonic stem cell.
  • the additional flanking BAL nucleic acid sequence is of sufficient length for successful homologous recombination with the endogenous gene.
  • homologous recombination nucleic acid molecule typically, several kilobases of flanking DNA (both at the 5' and 3' ends) are included in the homologous recombination nucleic acid molecule (see, e.g., Thomas, K.R. and Capecchi, M. R. (1987) Cell 51 :503 for a description of homologous recombination vectors).
  • the homologous recombination nucleic acid molecule is introduced into a cell, e.g., an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced BAL gene has homologously recombined with the endogenous BAL gene are selected (see e.g., Li, E. et al. (1992) Cell 69:915).
  • the selected cells can then injected into a blastocyst of an animal (e.g., a mouse) to form aggregation chimeras (see e.g., Bradley, A. in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, E.J. Robertson, ed. (IRL, Oxford, 1987) pp. 113-152).
  • a chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term.
  • Progeny harboring the homologously recombined DNA in their germ cells can be used to breed animals in which all cells of the animal contain the homologously recombined DNA by germline transmission of the transgene.
  • homologous recombination nucleic acid molecules e.g., vectors, or homologous recombinant animals are described further in Bradley, A. (1991) Current Opinion in Biotechnology 2:823-829 and in PCT International Publication Nos.: WO 90/11354 by Le Mouellec et al.; WO 91/01140 by Smithies et al.; WO 92/0968 by Zijlstra et al.; and WO 93/04169 by Berns et al.
  • transgenic non-humans animals can be produced which contain selected systems which allow for regulated expression of the transgene.
  • a system is the cre/loxP recombinase system of bacteriophage P 1.
  • Cre/loxP recombinase system of bacteriophage P 1.
  • FLP recombinase system of Saccharomyces cerevisiae (O'Gorman et al. (1991) Science 251 :1351-1355.
  • a cre/loxP recombinase system is used to regulate expression of the transgene
  • animals containing transgenes encoding both the Cre recombinase and a selected protein are required.
  • Such animals can be provided through the construction of "double" transgenic animals, e.g., by mating two transgenic animals, one containing a transgene encoding a selected protein and the other containing a transgene encoding a recombinase.
  • Clones of the non-human transgenic animals described herein can also be produced according to the methods described in Wilmut, I. et al. (1997) Nature 385:810- 813 and PCT International Publication Nos. WO 97/07668 and WO 97/07669.
  • a cell e.g., a somatic cell
  • the quiescent cell can then be fused, e.g., through the use of electrical pulses, to an enucleated oocyte from an animal of the same species from which the quiescent cell is isolated.
  • the recontructed oocyte is then cultured such that it develops to morula or blastocyte and then transferred to pseudopregnant female foster animal.
  • the offspring borne of this female foster animal will be a clone of the animal from which the cell, e.g., the somatic cell, is isolated.
  • compositions suitable for administration typically comprise the nucleic acid molecule, protein, or antibody and a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carrier is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration.
  • the use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.
  • a pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration.
  • routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), transmucosal, and rectal administration.
  • Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide.
  • a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents
  • antibacterial agents such as benzyl alcohol or methyl parabens
  • antioxidants
  • compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion.
  • suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF, Parsippany, NJ) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringability exists.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), and suitable mixtures thereof.
  • the proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like.
  • isotonic agents for example, sugars, polyalcohols such as manitol, sorbitol, sodium chloride in the composition.
  • Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
  • Sterile injectable solutions can be prepared by incorporating the active compound (e.g., a fragment of a BAL protein or an anti-BAL antibody) in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
  • the active compound e.g., a fragment of a BAL protein or an anti-BAL antibody
  • dispersions are prepared by incorporating the active compound into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above.
  • the preferred methods of preparation are vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • Oral compositions generally include an inert diluent or an edible carrier. They can be enclosed in gelatin capsules or compressed into tablets.
  • the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules, oral compositions can also be prepared using a fluid carrier for use as a mouthwash, wherein the compound in the fluid carrier is applied orally and swished and expectorated or swallowed.
  • Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition.
  • the tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, , methyl salicylate, or orange flavoring.
  • a suitable propellant e.g., a gas such as carbon dioxide, or a nebulizer.
  • Systemic administration can also be by transmucosal or transdermal means.
  • penetrants appropriate to the barrier to be permeated are used in the formulation.
  • penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives.
  • Transmucosal administration can be accomplished through the use of nasal sprays or suppositories.
  • the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.
  • the compounds can also be prepared in the form of suppositories (e.g., with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery.
  • suppositories e.g., with conventional suppository bases such as cocoa butter and other glycerides
  • retention enemas for rectal delivery.
  • the active compounds are prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems.
  • a controlled release formulation including implants and microencapsulated delivery systems.
  • Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. The materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc.
  • Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Patent No. 4,522,811.
  • Dosage unit form refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier.
  • the specification for the dosage unit forms of the invention are dictated by and directly dependent on the unique characteristics of the active compound and the particular therapeutic effect to be achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals.
  • Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population).
  • the dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50.
  • Compounds which exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.
  • the data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans.
  • the dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity.
  • the dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.
  • the therapeutically effective dose can be estimated initially from cell culture assays.
  • a dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture.
  • IC50 i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms
  • levels in plasma may be measured, for example, by high performance liquid chromatography.
  • the nucleic acid molecules of the invention can be inserted into vectors and used as gene therapy vectors.
  • Gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration (see U.S. Patent 5,328,470) or by stereotactic injection (see e.g., Chen et al. (1994) Proc. Natl. Acad. Sci. USA 91 :3054- 3057).
  • the pharmaceutical preparation of the gene therapy vector can include the gene therapy vector in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is imbedded.
  • the pharmaceutical preparation can include one or more cells which produce the gene delivery system.
  • compositions can be included in a container, pack, or dispenser together with instructions for administration.
  • nucleic acid molecules, proteins, protein homologues, and antibodies described herein can be used in one or more of the following methods: a) screening assays; b) predictive medicine (e.g., diagnostic assays, prognostic assays, monitoring clinical trials, and pharmacogenetics); and c) methods of treatment (e.g., therapeutic and prophylactic).
  • a BAL protein of the invention has one or more of the following activities: (1) it interacts with a non-BAL protein molecule, e.g., CRK, CRK-L, SHP-2, PI3K, or ZAP70; (2) it activates a BAL-dependent signal transduction pathway; (3) it modulates the occurrence and severity of a malignancy such as a lymphoma, e.g., non-Hodgkin's lymphoma; and (4) it modulates cell migration, motility, and shape, as well as cell/cell and cell/extra-cellular matrix interactions, and, thus, can be used to, for example, (1) modulate the interaction with a non-BAL protein molecule; (2) activate a BAL-dependent signal transduction pathway; (3) modulate the occurrence and severity of a malignancy such as a lymphoma, e.g., non-Hodgkin's lymphoma; and (4) modulate cell migration, motility, and shape, as well as
  • the isolated nucleic acid molecules of the invention can be used, for example, to express BAL protein (e.g., via a recombinant expression vector in a host cell in gene therapy applications), to detect BAL mRNA (e.g., in a biological sample) or a genetic alteration in a BAL gene, and to modulate BAL activity, as described further below.
  • BAL proteins can be used to treat disorders characterized by insufficient or excessive production of a BAL substrate or production of BAL inhibitors.
  • the BAL proteins can be used to screen for naturally occurring BAL substrates, to screen for drugs or compounds which modulate BAL activity, as well as to treat disorders characterized by insufficient or excessive production of BAL protein or production of BAL protein forms which have decreased or aberrant activity compared to BAL wild type protein (e.g., Non-Hodgkin's lymphoma).
  • BAL wild type protein e.g., Non-Hodgkin's lymphoma
  • the anti-BAL antibodies of the invention can be used to detect and isolate BAL proteins, regulate the bioavailability of BAL proteins, and modulate BAL activity.
  • the invention provides a method (also referred to herein as a "screening assay") for identifying and/or producing modulators, /. e. , candidate or test compounds or agents (e.g., peptides, peptidomimetics, small molecules or other drugs) which bind to BAL proteins, have a stimulatory or inhibitory effect on, for example, BAL expression or BAL activity, or have a stimulatory or inhibitory effect on, for example, the expression or activity of a BAL substrate.
  • modulators /. e. , candidate or test compounds or agents (e.g., peptides, peptidomimetics, small molecules or other drugs) which bind to BAL proteins, have a stimulatory or inhibitory effect on, for example, BAL expression or BAL activity, or have a stimulatory or inhibitory effect on, for example, the expression or activity of a BAL substrate.
  • the invention provides assays for screening candidate or test compounds which are substrates of a BAL protein or polypeptide or biologically active portion thereof. In another embodiment, the invention provides assays for screening candidate or test compounds which bind to or modulate the activity of a BAL protein or polypeptide or biologically active portion thereof.
  • the test compounds of the present invention can be obtained using any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the 'one-bead one-compound' library method; and synthetic library methods using affinity chromatography selection.
  • the biological library approach is limited to peptide libraries, while the other four approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounds (Lam, K.S. (1997) Anticancer Drug Des. 12:145).
  • Biotechniques 13:412-421 or on beads (Lam (1991) Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556), bacteria (Ladner USP 5,223,409), spores (Ladner USP '409), plasmids (Cull et al. (1992) Proc Natl Acad Sci USA 89:1865-1869) or on phage (Scott and Smith (1990) Science 249:386-390); (Devlin (1990) Science 249:404-406); (Cwirla et al. (1990) Proc. Natl. Acad. Sci. 87:6378-6382); (Felici (1991) J. Mol. Biol. 222:301-310); (Ladner supra.).
  • an assay is a cell-based assay in which a cell which expresses a BAL protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to modulate BAL activity is determined. Determining the ability of the test compound to modulate BAL activity can be accomplished by monitoring, for example, the survival of a cell which expresses BAL or the activity of a B AL-regulated transcription factor.
  • the cell for example, can be of mammalian origin, e.g., a peripheral blood cell.
  • the ability of the test compound to modulate BAL binding to a substrate or to bind to BAL can also be determined. Determining the ability of the test compound to modulate BAL binding to a substrate can be accomplished, for example, by coupling the BAL substrate with a radioisotope or enzymatic label such that binding of the BAL substrate to BAL can be determined by detecting the labeled BAL substrate in a complex. Determining the ability of the test compound to bind BAL can be accomplished, for example, by coupling the compound with a radioisotope or enzymatic label such that binding of the compound to BAL can be determined by detecting the labeled BAL compound in a complex.
  • compounds e.g., BAL substrates
  • compounds can be labeled with 125j 5 35 ⁇ ? 14 or 3J J ? i her directly or indirectly, and the radioisotope detected by direct counting of radioemmission or by scintillation counting.
  • compounds can be enzymatically labeled with, for example, horseradish peroxidase, alkaline phosphatase, or luciferase, and the enzymatic label detected by determination of conversion of an appropriate substrate to product.
  • a microphysiometer can be used to detect the interaction of a compound with BAL without the labeling of either the compound or the BAL. McConnell, H. M. et al. (1992) Science 257:1906-1912.
  • a "microphysiometer” e.g., Cytosensor
  • LAPS light-addressable potentiometric sensor
  • an assay is a cell-based assay comprising contacting a cell expressing a BAL target molecule (e.g., a BAL substrate) with a test compound and determining the ability of the test compound to modulate (e.g. stimulate or inhibit) the activity of the BAL target molecule. Determining the ability of the test compound to modulate the activity of a BAL target molecule can be accomplished, for example, by determining the ability of the BAL protein to bind to or interact with the BAL target molecule.
  • a BAL target molecule e.g., a BAL substrate
  • Determining the ability of the BAL protein or a biologically active fragment thereof, to bind to or interact with a BAL target molecule can be accomplished by one of the methods described above for determining direct binding. In a preferred embodiment, determining the ability of the BAL protein to bind to or interact with a BAL target molecule can be accomplished by determining the activity of the target molecule.
  • the activity of the target molecule can be determined by detecting induction of a cellular second messenger of the target (i.e., intracellular Ca2 + , diacylglycerol, IP3, and the like), detecting catalytic/enzymatic activity of the target an appropriate substrate, detecting the induction of a reporter gene (comprising a target-responsive regulatory element operatively linked to a nucleic acid encoding a detectable marker, e.g., luciferase), or detecting a target-regulated cellular response.
  • a cellular second messenger of the target i.e., intracellular Ca2 + , diacylglycerol, IP3, and the like
  • detecting catalytic/enzymatic activity of the target an appropriate substrate detecting the induction of a reporter gene (comprising a target-responsive regulatory element operatively linked to a nucleic acid encoding a detectable marker, e.g., luciferase), or detecting a target-regulated
  • an assay of the present invention is a cell-free assay in which a BAL protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to bind to the BAL protein or biologically active portion thereof is determined.
  • Preferred biologically active portions of the BAL proteins to be used in assays of the present invention include fragments which participate in interactions with non-BAL molecules, e.g., fragments with high surface probability scores. Binding of the test compound to the BAL protein can be determined either directly or indirectly as described above.
  • the assay includes contacting the BAL protein or biologically active portion thereof with a known compound which binds BAL to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with a BAL protein, wherein determining the ability of the test compound to interact with a BAL protein comprises determining the ability of the test compound to preferentially bind to BAL or biologically active portion thereof as compared to the known compound.
  • the assay is a cell-free assay in which a BAL protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to modulate (e.g., stimulate or inhibit) the activity of the BAL protein or biologically active portion thereof is determined.
  • Determining the ability of the test compound to modulate the activity of a BAL protein can be accomplished, for example, by determining the ability of the BAL protein to bind to a BAL target molecule by one of the methods described above for determining direct binding. Determining the ability of the BAL protein to bind to a BAL target molecule can also be accomplished using a technology such as real-time Biomolecular Interaction Analysis (BIA). Sjolander, S. and Urbaniczky, C.
  • BIOA is a technology for studying biospecific interactions in real time, without labeling any of the interactants (e.g., BIAcore). Changes in the optical phenomenon of surface plasmon resonance (SPR) can be used as an indication of real-time reactions between biological molecules.
  • SPR surface plasmon resonance
  • determining the ability of the test compound to modulate the activity of a BAL protein can be accomplished by determining the ability of the BAL protein to further modulate the activity of a downstream effector of a BAL target molecule.
  • the activity of the effector molecule on an appropriate target can be determined or the binding of the effector to an appropriate target can be determined as previously described.
  • the cell-free assays of the present invention are amenable to use of both soluble and/or membrane-bound forms of isolated proteins (e.g., BAL proteins or biologically active portions thereof ).
  • isolated proteins e.g., BAL proteins or biologically active portions thereof.
  • non-ionic detergents such as n- oc
  • binding of a test compound to a BAL protein, or interaction of a BAL protein with a target molecule in the presence and absence of a candidate compound can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microtitre plates, test tubes, and micro-centrifuge tubes.
  • a fusion protein can be provided which adds a domain that allows one or both of the proteins to be bound to a matrix.
  • glutathione-S-transferase/ BAL fusion proteins or glutathione-S- transferase/target fusion proteins can be adsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis, MO) or glutathione derivatized microtitre plates, which are then combined with the test compound or the test compound and either the non-adsorbed target protein or BAL protein, and the mixture incubated under conditions conducive to complex formation (e.g., at physiological conditions for salt and pH). Following incubation, the beads or microtitre plate wells are washed to remove any unbound components, the matrix immobilized in the case of beads, complex determined either directly or indirectly, for example, as described above. Alternatively, the complexes can be dissociated from the matrix, and the level of BAL binding or activity determined using standard techniques.
  • a BAL protein or a BAL target molecule can be immobilized utilizing conjugation of biotin and streptavidin.
  • Biotinylated BAL protein or target molecules can be prepared from biotin-NHS (N- hydroxy-succinimide) using techniques known in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, IL), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical).
  • biotinylation kit Pierce Chemicals, Rockford, IL
  • streptavidin-coated 96 well plates Piereptavidin-coated 96 well plates
  • antibodies reactive with BAL protein or target molecules but which do not interfere with binding of the BAL protein to its target molecule can be derivatized to the wells of the plate, and unbound target or BAL protein trapped in the wells by antibody conjugation.
  • Methods for detecting such complexes include immunodetection of complexes using antibodies reactive with the BAL protein or target molecule, as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the BAL protein or target molecule.
  • modulators of BAL expression are produced or identified in a method wherein a cell is contacted with a candidate compound and the expression of BAL mRNA or protein in the cell is determined.
  • the level of expression of BAL mRNA or protein in the presence of the candidate compound is compared to the level of expression of BAL mRNA or protein in the absence of the candidate compound.
  • the candidate compound can then be produced or identified as a modulator of BAL expression based on this comparison. For example, when expression of BAL mRNA or protein is greater (statistically significantly greater) in the presence of the candidate compound than in its absence, the candidate compound is identified as a stimulator of BAL mRNA or protein expression (i. e. a stimulator of BAL mRNA or protein expression is produced).
  • the candidate compound when expression of BAL mRNA or protein is less (statistically significantly less) in the presence of the candidate compound than in its absence, the candidate compound is produced or identified as an inhibitor of BAL mRNA or protein expression (i.e. an inhibitor of BAL mRNA or protein expression is produced).
  • the level of BAL mRNA or protein expression in the cells can be determined by methods described herein for detecting BAL mRNA or protein.
  • the BAL proteins can be used as "bait proteins" in a two-hybrid assay or three-hybrid assay (see, e.g., U.S. Patent No. 5,283,317; Zervos et al. (1993) Cell 72:223-232; Madura et al. (1993) J. Biol. Chem. 268:12046-12054; Bartel et al. (1993) Biotechniques 14:920-924; Iwabuchi et al.
  • BAL-binding proteins proteins which bind to or interact with BAL
  • BAL-binding proteins proteins which bind to or interact with BAL
  • BAL-binding proteins are also likely to be involved in the propagation of signals by the BAL proteins or BAL targets as, for example, downstream elements of a B AL-mediated signaling pathway.
  • BAL-binding proteins are likely to be BAL inhibitors.
  • the two-hybrid system is based on the modular nature of most transcription factors, which consist of separable DNA-binding and activation domains.
  • the assay utilizes two different DNA constructs.
  • the gene that codes for a BAL protein is fused to a gene encoding the DNA binding domain of a known transcription factor (e.g., GAL-4).
  • a DNA sequence, from a library of DNA sequences, that encodes an unidentified protein (“prey" or "sample”) is fused to a gene that codes for the activation domain of the known transcription factor.
  • the DNA-binding and activation domains of the transcription factor are brought into close proximity. This proximity allows transcription of a reporter gene (e.g, LacZ) which is operably linked to a transcriptional regulatory site responsive to the transcription factor. Expression of the reporter gene can be detected and cell colonies containing the functional transcription factor can be isolated and used to obtain the cloned gene which encodes the protein which interacts with the BAL protein.
  • a reporter gene e.g, LacZ
  • Expression of the reporter gene can be detected and cell colonies containing the functional transcription factor can be isolated and used to obtain the cloned gene which encodes the protein which interacts with the BAL protein.
  • This invention further pertains to novel agents identified by the above-described screening assays. Accordingly, it is within the scope of this invention to further use an agent identified and/or produced as described herein in an appropriate animal model.
  • an agent identified and/or produced as described herein e.g., a BAL modulating agent, an antisense BAL nucleic acid molecule, a BAL-specific antibody, or a BAL-binding partner
  • an agent identified and/or produced as described herein can be used in an animal model to determine the efficacy, toxicity, or side effects of treatment with such an agent.
  • an agent identified and/or produced as described herein can be used in an animal model to determine the mechanism of action of such an agent.
  • this invention pertains to uses of novel agents identified and/or produced by the above-described screening assays for treatments as described herein.
  • cDNA sequences identified herein can be used in numerous ways as polynucleotide reagents. For example, these sequences can be used to: (i) map their respective genes on a chromosome; and, thus, locate gene regions associated with genetic disease; (ii) identify an individual from a minute biological sample (tissue typing); and (iii) aid in forensic identification of a biological sample. These applications are described in the subsections below.
  • this sequence can be used to map the location of the gene on a chromosome.
  • This process is called chromosome mapping.
  • portions or fragments of the BAL nucleotide sequences, described herein can be used to map the location of the BAL genes on a chromosome (further described in Example 1, below).
  • the mapping of the BAL sequences to chromosomes is an important first step in correlating these sequences with genes associated with disease.
  • BAL genes can be mapped to chromosomes by preparing PCR primers (preferably 15-25 bp in length) from the BAL nucleotide sequences. Computer analysis of the BAL sequences can be used to predict primers that do not span more than one exon in the genomic DNA, thus complicating the amplification process. These primers can then be used for PCR screening of somatic cell hybrids containing individual human chromosomes. Only those hybrids containing the human gene corresponding to the BAL sequences will yield an amplified fragment. Somatic cell hybrids are prepared by fusing somatic cells from different mammals (e.g., human and mouse cells).
  • PCR mapping of somatic cell hybrids is a rapid procedure for assigning a particular sequence to a particular chromosome. Three or more sequences can be assigned per day using a single thermal cycler. Using the BAL nucleotide sequences to design oligonucleotide primers, sublocalization can be achieved with panels of fragments from specific chromosomes. Other mapping strategies which can similarly be used to map a BAL sequence to its chromosome include in situ hybridization (described in Fan, Y. et al. (1990) Proc. Natl. Acad. Sci.
  • FISH Fluorescence in situ hybridization
  • Chromosome spreads can be made using cells whose division has been blocked in metaphase by a chemical such as colcemid that disrupts the mitotic spindle.
  • the chromosomes can be treated briefly with trypsin, and then stained with Giemsa. A pattern of light and dark bands develops on each chromosome, so that the chromosomes can be identified individually.
  • the FISH technique can be used with a DNA sequence as short as 500 or 600 bases. However, clones larger than 1,000 bases have a higher likelihood of binding to a unique chromosomal location with sufficient signal intensity for simple detection. Preferably 1,000 bases, and more preferably 2,000 bases will suffice to get good results at a reasonable amount of time. For a review of this technique, see Verma et al., Human Chromosomes: A Manual of Basic Techniques (Pergamon Press, New York 1988).
  • Reagents for chromosome mapping can be used individually to mark a single chromosome or a single site on that chromosome, or panels of reagents can be used for marking multiple sites and/or multiple chromosomes. Reagents corresponding to noncoding regions of the genes actually are preferred for mapping purposes. Coding sequences are more likely to be conserved within gene families, thus increasing the chance of cross hybridizations during chromosomal mapping. Once a sequence has been mapped to a precise chromosomal location, the physical position of the sequence on the chromosome can be correlated with genetic map data. (Such data are found, for example, in V.
  • differences in the DNA sequences between individuals affected and unaffected with a disease associated with the BAL gene can be determined. If a mutation is observed in some or all of the affected individuals but not in any unaffected individuals, then the mutation is likely to be the causative agent of the particular disease. Comparison of affected and unaffected individuals generally involves first looking for structural alterations in the chromosomes, such as deletions or translocations that are visible from chromosome spreads or detectable using PCR based on that DNA sequence. Ultimately, complete sequencing of genes from several individuals can be performed to confirm the presence of a mutation and to distinguish mutations from polymorphisms.
  • the BAL sequences of the present invention can also be used to identify individuals from minute biological samples.
  • the United States military for example, is considering the use of restriction fragment length polymorphism (RFLP) for identification of its personnel.
  • RFLP restriction fragment length polymorphism
  • an individual's genomic DNA is digested with one or more restriction enzymes, and probed on a Southern blot to yield unique bands for identification.
  • This method does not suffer from the current limitations of "Dog Tags" which can be lost, switched, or stolen, making positive identification difficult.
  • the sequences of the present invention are useful as additional DNA markers for RFLP (described in U.S. Patent 5,272,057).
  • sequences of the present invention can be used to provide an alternative technique which determines the actual base-by-base DNA sequence of selected portions of an individual's genome.
  • the BAL nucleotide sequences described herein can be used to prepare two PCR primers from the 5' and 3' ends of the sequences. These primers can then be used to amplify an individual's DNA and subsequently sequence it.
  • Panels of corresponding DNA sequences from individuals, prepared in this manner, can provide unique individual identifications, as each individual will have a unique set of such DNA sequences due to allelic differences.
  • the sequences of the present invention can be used to obtain such identification sequences from individuals and from tissue.
  • the BAL nucleotide sequences of the invention uniquely represent portions of the human genome. Allelic variation occurs to some degree in the coding regions of these sequences, and to a greater degree in the noncoding regions. It is estimated that allelic variation between individual humans occurs with a frequency of about once per each 500 bases.
  • Each of the sequences described herein can, to some degree, be used as a standard against which DNA from an individual can be compared for identification purposes.
  • the noncoding sequences of SEQ ID NOJ or 4 can comfortably provide positive individual identification with a panel of perhaps 10 to 1,000 primers which each yield a noncoding amplified sequence of 100 bases. If predicted coding sequences, such as those in SEQ ID NOJ or 6 are used, a more appropriate number of primers for positive individual identification would be 500-2,000.
  • a panel of reagents from BAL nucleotide sequences described herein is used to generate a unique identification database for an individual, those same reagents can later be used to identify tissue from that individual.
  • Using the unique identification database positive identification of the individual, living or dead, can be made from extremely small tissue samples.
  • Forensic biology is a scientific field employing genetic typing of biological evidence found at a crime scene as a means for positively identifying, for example, a perpetrator of a crime.
  • PCR technology can be used to amplify DNA sequences taken from very small biological samples such as tissues, e.g., hair or skin, or body fluids, e.g. , blood, saliva, or semen found at a crime scene.
  • the amplified sequence can then be compared to a standard, thereby allowing identification of the origin of the biological sample.
  • sequences of the present invention can be used to provide polynucleotide reagents, e.g., PCR primers, targeted to specific loci in the human genome, which can enhance the reliability of DNA-based forensic identifications by, for example, providing another "identification marker" (i.e. another DNA sequence that is unique to a particular individual).
  • an "identification marker” i.e. another DNA sequence that is unique to a particular individual.
  • actual base sequence information can be used for identification as an accurate alternative to patterns formed by restriction enzyme generated fragments.
  • Sequences targeted to noncoding regions of SEQ ID NOJ or 4 are particularly appropriate for this use as greater numbers of polymorphisms occur in the noncoding regions, making it easier to differentiate individuals using this technique.
  • polynucleotide reagents include the BAL nucleotide sequences or portions thereof, e.g., fragments derived from the noncoding regions of SEQ ID NOJ or 4 having a length of at least 20 bases, preferably at least 30 bases.
  • the BAL nucleotide sequences described herein can further be used to provide polynucleotide reagents, e.g., labeled or labelable probes which can be used in, for example, an in situ hybridization technique, to identify a specific tissue, e.g., brain tissue. This can be very useful in cases where a forensic pathologist is presented with a tissue of unknown origin. Panels of such BAL probes can be used to identify tissue by species and/or by organ type. In a similar fashion, these reagents, e.g., BAL primers or probes can be used to screen tissue culture for contamination (i.e. screen for the presence of a mixture of different types of cells in a culture).
  • the present invention also pertains to the field of predictive medicine in which diagnostic assays, prognostic assays, and monitoring clinical trials are used for prognostic (predictive) purposes to thereby treat an individual prophylactically. Accordingly, one aspect of the present invention relates to diagnostic assays for determining BAL protein and/or nucleic acid expression as well as BAL activity, in the context of a biological sample (e.g., blood, serum, cells, tissue) to thereby determine whether an individual is afflicted with a disease or disorder, or is at risk of developing a disorder, associated with aberrant BAL expression or activity, e.g., a malignancy such as a lymphoma, e.g., non-Hodgkin's lymphoma.
  • a biological sample e.g., blood, serum, cells, tissue
  • the invention also provides for prognostic (or predictive) assays for determining whether an individual is at risk of developing a disorder associated with BAL protein, nucleic acid expression or activity. For example, mutations in a BAL gene can be assayed in a biological sample. Such assays can be used for prognostic or predictive purpose to thereby phophylactically treat an individual prior to the onset of a disorder characterized by or associated with BAL protein, nucleic acid expression or activity e.g., a malignancy such as a lymphoma, e.g., non-Hodgkin's lymphoma.
  • Another aspect of the invention pertains to monitoring the influence of agents (e.g., drugs, compounds) on the expression or activity of BAL in clinical trials.
  • An exemplary method for detecting the presence or absence of BAL protein or nucleic acid in a biological sample involves obtaining a biological sample from a test subject and contacting the biological sample with a compound or an agent capable of detecting BAL protein or nucleic acid (e.g., mRNA or genomic DNA) that encodes BAL protein such that the presence of BAL protein or nucleic acid is detected in the biological sample.
  • a compound or an agent capable of detecting BAL protein or nucleic acid e.g., mRNA or genomic DNA
  • a preferred agent for detecting BAL mRNA or genomic DNA is a labeled nucleic acid probe capable of hybridizing to BAL mRNA or genomic DNA.
  • the nucleic acid probe can be, for example, a full-length BAL nucleic acid, such as the nucleic acid of SEQ ID NOJ, 3, 4, or 6, or a portion thereof, such as an oligonucleotide of at least 15, 30, 50, 100, 250 or 500 nucleotides in length and sufficient to specifically hybridize under stringent conditions to BAL mRNA or genomic DNA.
  • a full-length BAL nucleic acid such as the nucleic acid of SEQ ID NOJ, 3, 4, or 6, or a portion thereof, such as an oligonucleotide of at least 15, 30, 50, 100, 250 or 500 nucleotides in length and sufficient to specifically hybridize under stringent conditions to BAL mRNA or genomic DNA.
  • Other suitable probes for use in the diagnostic assays of the invention are described herein.
  • a preferred agent for detecting BAL protein is an antibody capable of binding to BAL protein, preferably an antibody with a detectable label.
  • Antibodies can be polyclonal, or more preferably, monoclonal. An intact antibody, or a fragment thereof (e.g., Fab or F(ab')2) can be used.
  • the term "labeled", with regard to the probe or antibody, is intended to encompass direct labeling of the probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling of the probe or antibody by reactivity with another reagent that is directly labeled.
  • Examples of indirect labeling include detection of a primary antibody using a fluorescently labeled secondary antibody and end-labeling of a DNA probe with biotin such that it can be detected with fluorescently labeled streptavidin.
  • biological sample is intended to include tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject. That is, the detection method of the invention can be used to detect BAL mRNA, protein, or genomic DNA in a biological sample in vitro as well as in vivo.
  • in vitro techniques for detection of BAL mRNA include Northern hybridizations and in situ hybridizations.
  • In vitro techniques for detection of BAL protein include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations and immunofluorescence.
  • In vitro techniques for detection of BAL genomic DNA include Southern hybridizations.
  • in vivo techniques for detection of BAL protein include introducing into a subject a labeled anti-BAL antibody.
  • the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques.
  • the biological sample contains protein molecules from the test subject.
  • the biological sample can contain mRNA molecules from the test subject or genomic DNA molecules from the test subject.
  • a preferred biological sample is a serum sample isolated by conventional means from a subject.
  • the methods further involve obtaining a control biological sample from a control subject, contacting the control sample with a compound or agent capable of detecting BAL protein, mRNA, or genomic DNA, such that the presence of BAL protein, mRNA or genomic DNA is detected in the biological sample, and comparing the presence of BAL protein, mRNA or genomic DNA in the control sample with the presence of BAL protein, mRNA or genomic DNA in the test sample.
  • a compound or agent capable of detecting BAL protein, mRNA, or genomic DNA such that the presence of BAL protein, mRNA or genomic DNA is detected in the biological sample
  • the invention also encompasses kits for detecting the presence of BAL in a biological sample.
  • the kit can comprise a labeled compound or agent capable of detecting BAL protein or mRNA in a biological sample; means for determining the amount of BAL in the sample; and means for comparing the amount of BAL in the sample with a standard.
  • the compound or agent can be packaged in a suitable container.
  • the kit can further comprise instructions for using the kit to detect BAL protein or nucleic acid.
  • the diagnostic methods described herein can furthermore be utilized to identify subjects having or at risk of developing a disease or disorder associated with aberrant BAL expression or activity e.g., a malignancy such as a lymphoma, e.g., non-Hodgkin's lymphoma.
  • a malignancy such as a lymphoma, e.g., non-Hodgkin's lymphoma.
  • the term "aberrant” includes a BAL expression or activity which deviates from the wild type BAL expression or activity. Aberrant expression or activity includes increased or decreased expression or activity, as well as expression or activity which does not follow the wild type developmental pattern of expression or the subcellular pattern of expression.
  • aberrant BAL expression or activity is intended to include the cases in which a mutation in the BAL gene causes the BAL gene to be under-expressed or over-expressed and situations in which such mutations result in a non-functional BAL protein or a protein which does not function in a wild-type fashion, e.g., a protein which does not interact with a BAL ligand or one which interacts with a non-BAL ligand.
  • the assays described herein can be utilized to identify a subject having or at risk of developing a disorder associated with a misregulation in BAL protein activity or nucleic acid expression, e.g., a malignancy such as a lymphoma, e.g., non-Hodgkin's lymphoma.
  • a malignancy such as a lymphoma
  • the prognostic assays can be utilized to identify a subject having or at risk for developing a disorder associated with a misregulation in BAL protein activity or nucleic acid expression, such as a e.g., a malignancy such as a lymphoma, e.g., non- Hodgkin's lymphoma.
  • the present invention provides a method for identifying a disease or disorder associated with aberrant BAL expression or activity in which a test sample is obtained from a subject and BAL protein or nucleic acid (e.g., mRNA or genomic DNA) is detected, wherein the presence of BAL protein or nucleic acid is diagnostic for a subject having or at risk of developing a disease or disorder associated with aberrant BAL expression or activity.
  • a test sample refers to a biological sample obtained from a subject of interest.
  • a test sample can be a biological fluid (e.g., serum), cell sample, or tissue.
  • the prognostic assays described herein can be used to determine whether a subject can be administered an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate) to treat a disease or disorder associated with aberrant BAL expression or activity.
  • an agent e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate
  • a subject can be effectively treated with an agent for a e.g., a malignancy such as a lymphoma, e.g., non-Hodgkin's lymphoma.
  • the present invention provides methods for determining whether a subject can be effectively treated with an agent for a disorder associated with aberrant BAL expression or activity in which a test sample is obtained and BAL protein or nucleic acid expression or activity is detected (e.g., wherein the abundance of BAL protein or nucleic acid expression or activity is diagnostic for a subject that can be administered the agent to treat a disorder associated with aberrant BAL expression or activity).
  • the methods of the invention can also be used to detect genetic alterations in a BAL gene, thereby determining if a subject with the altered gene is at risk for a disorder characterized by misregulation in BAL protein activity or nucleic acid expression, such as a e.g., a malignancy such as a lymphoma, e.g., non-Hodgkin's lymphoma.
  • the methods include detecting, in a sample of cells from the subject, the presence or absence of a genetic alteration characterized by at least one of an alteration affecting the integrity of a gene encoding a B AL-protein, or the mis- expression of the BAL gene.
  • such genetic alterations can be detected by ascertaining the existence of at least one of 1) a deletion of one or more nucleotides from a BAL gene; 2) an addition of one or more nucleotides to a BAL gene; 3) a substitution of one or more nucleotides of a BAL gene, 4) a chromosomal rearrangement of a BAL gene; 5) an alteration in the level of a messenger RNA transcript of a BAL gene, 6) aberrant modification of a BAL gene, such as of the methylation pattern of the genomic DNA, 7) the presence of a non- wild type splicing pattern of a messenger RNA transcript of a BAL gene, 8) a non- wild type level of a B AL-protein, 9) allelic loss of a BAL gene, and 10) inappropriate post-translational modification of a B AL-protein.
  • assays known in the art which can be used for detecting alterations in a
  • detection of the alteration involves the use of a probe/primer in a polymerase chain reaction (PCR) (see, e.g., U.S. Patent Nos. 4,683,195 and 4,683,202), such as anchor PCR or RACE PCR, or, alternatively, in a ligation chain reaction (LCR) (see, e.g., Landegran et al. (1988) Science 241 J077-1080; and Nakazawa et al. (1994) Proc. Natl. Acad. Sci. USA 91 J60-364), the latter of which can be particularly useful for detecting point mutations in the BAL-gene (see Abravaya et al.
  • PCR polymerase chain reaction
  • LCR ligation chain reaction
  • This method can include the steps of collecting a sample of cells from a subject, isolating nucleic acid (e.g., genomic DNA or mRNA) from the cells of the sample, contacting the nucleic acid sample with one or more primers which specifically hybridize to a BAL gene under conditions such that hybridization and amplification of the BAL-gene (if present) occurs, and detecting the presence or absence of an amplification product, or detecting the size of the amplification product and comparing the length to a control sample. It is anticipated that PCR and/or LCR may be desirable to use as a preliminary amplification step in conjunction with any of the techniques used for detecting mutations described herein.
  • nucleic acid e.g., genomic DNA or mRNA
  • Alternative amplification methods include: self sustained sequence replication (Guatelli, J.C. et al, (1990) Proc. Natl. Acad. Sci. USA 87:1874-1878), transcriptional amplification system (Kwoh, D.Y. et al, (1989) Proc. Natl. Acad. Sci. USA 86:1173- 1177), Q-Beta Replicase (Lizardi, P.M. et al. (1988) Bio-Technology 6:1197), or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers.
  • mutations in a BAL gene from a sample cell can be identified by alterations in restriction enzyme cleavage patterns.
  • sample and control DNA is isolated, amplified (optionally), digested with one or more restriction endonucleases, and fragment length sizes are determined by gel electrophoresis and compared. Differences in fragment length sizes between sample and control DNA indicates mutations in the sample DNA.
  • sequence specific ribozymes see, for example, U.S. Patent No. 5,498,531 can be used to score for the presence of specific mutations by development or loss of a ribozyme cleavage site.
  • genetic mutations in BAL can be identified by hybridizing a sample and control nucleic acids, e.g., DNA or RNA, to high density arrays containing hundreds or thousands of oligonucleotides probes (Cronin, M.T. et al. (1996) Human Mutation 1: 244-255; Kozal, M.J. et al. (1996) Nature Medicine 2: 753- 759).
  • genetic mutations in BAL can be identified in two dimensional arrays containing light-generated DNA probes as described in Cronin, M.T. et al. supra.
  • a first hybridization array of probes can be used to scan through long stretches of DNA in a sample and control to identify base changes between the sequences by making linear arrays of sequential overlapping probes. This step allows the identification of point mutations. This step is followed by a second hybridization array that allows the characterization of specific mutations by using smaller, specialized probe arrays complementary to all variants or mutations detected.
  • Each mutation array is composed of parallel probe sets, one complementary to the wild-type gene and the other complementary to the mutant gene.
  • any of a variety of sequencing reactions known in the art can be used to directly sequence the BAL gene and detect mutations by comparing the sequence of the sample BAL with the corresponding wild-type (control) sequence.
  • Examples of sequencing reactions include those based on techniques developed by Maxam and Gilbert ((1977) Proc. Natl Acad. Sci. USA 74:560) or Sanger ((1977) Proc. Natl. Acad. Sci. USA 74:5463). It is also contemplated that any of a variety of automated sequencing procedures can be used when performing the diagnostic assays ((1995) Biotechniques 19:448), including sequencing by mass spectrometry (see, e.g., PCT International Publication No. WO 94/16101; Cohen et al. (1996) Adv. Chromatogr. 36:127-162; and Griffin et al. (1993) Appl Biochem. Biotechnol 38:147- 159).
  • RNA RNA or RNA/DNA heteroduplexes Other methods for detecting mutations in the BAL gene include methods in which protection from cleavage agents is used to detect mismatched bases in RNA RNA or RNA/DNA heteroduplexes (Myers et al. (1985) Science 230:1242).
  • the art technique of "mismatch cleavage" starts by providing heteroduplexes of formed by hybridizing (labeled) RNA or DNA containing the wild-type BAL sequence with potentially mutant RNA or DNA obtained from a tissue sample.
  • the double-stranded duplexes are treated with an agent which cleaves single-stranded regions of the duplex such as which will exist due to basepair mismatches between the control and sample strands.
  • RNA/DNA duplexes can be treated with RNase and DNA/DNA hybrids treated with SI nuclease to enzymatically digesting the mismatched regions.
  • either DNA/DNA or RNA/DNA duplexes can be treated with hydroxylamine or osmium tetroxide and with piperidine in order to digest mismatched regions. After digestion of the mismatched regions, the resulting material is then separated by size on denaturing polyacrylamide gels to determine the site of mutation. See, for example, Cotton et al. (1988) Proc. Natl. Acad. Sci. USA 85:4397; Saleeba et al. (1992) Methods Enzymol. 217:286-295.
  • the control DNA or RNA can be labeled for detection.
  • the mismatch cleavage reaction employs one or more proteins that recognize mismatched base pairs in double-stranded DNA (so called "DNA mismatch repair" enzymes) in defined systems for detecting and mapping point mutations in BAL cDNAs obtained from samples of cells.
  • DNA mismatch repair enzymes
  • the mutY enzyme of E. coli cleaves A at G/A mismatches and the thymidine DNA glycosylase from HeLa cells cleaves T at G/T mismatches (Hsu et al. (1994) Carcinogenesis 15:1657-1662).
  • a probe based on a BAL sequence e.g.
  • a wild-type BAL sequence is hybridized to a cDNA or other DNA product from a test cell(s).
  • the duplex is treated with a DNA mismatch repair enzyme, and the cleavage products, if any, can be detected from electrophoresis protocols or the like. See, for example, U.S. Patent No. 5,459,039.
  • alterations in electrophoretic mobility will be used to identify mutations in BAL genes.
  • single strand conformation polymorphism SSCP
  • SSCP single strand conformation polymorphism
  • Single-stranded DNA fragments of sample and control BAL nucleic acids will be denatured and allowed to renature.
  • the secondary structure of single-stranded nucleic acids varies according to sequence, the resulting alteration in electrophoretic mobility enables the detection of even a single base change.
  • the DNA fragments may be labeled or detected with labeled probes.
  • the sensitivity of the assay may be enhanced by using RNA (rather than DNA), in which the secondary structure is more sensitive to a change in sequence.
  • the subject method uses heteroduplex analysis to separate double stranded heteroduplex molecules on the basis of changes in electrophoretic mobility (Keen et al. (1991) Trends Genet. 7:5).
  • DGGE denaturing gradient gel electrophoresis
  • DGGE DGGE is used as the method of analysis, DNA will be modified to insure that it does not completely denature, for example by adding a GC clamp of approximately 40 bp of high-melting GC-rich DNA by PCR.
  • a temperature gradient is used in place of a denaturing gradient to identify differences in the mobility of control and sample DNA (Rosenbaum and Reissner (1987) Biophys. Chem. 265:12753).
  • oligonucleotide primers may be prepared in which the known mutation is placed centrally and then hybridized to target DNA under conditions which permit hybridization only if a perfect match is found (Saiki et al. ( 1986) Nature 324:163); Saiki et al. (1989) Proc. Natl Acad. Sci. USA 86:6230).
  • Such allele specific oligonucleotides are hybridized to PCR amplified target DNA or a number of different mutations when the oligonucleotides are attached to the hybridizing membrane and hybridized with labeled target DNA.
  • allele specific amplification technology which depends on selective
  • PCR amplification may be used in conjunction with the instant invention.
  • Oligonucleotides used as primers for specific amplification may carry the mutation of interest in the center of the molecule (so that amplification depends on differential hybridization) (Gibbs et al. (1989) Nucleic Acids Res. 17:2437-2448) or at the extreme 3' end of one primer where, under appropriate conditions, mismatch can prevent, or reduce polymerase extension (Prossner (1993) Tibtech 11 :238).
  • it may be desirable to introduce a novel restriction site in the region of the mutation to create cleavage-based detection Gasparini et al. (1992) Mol. Cell Probes 6:1).
  • amplification may also be performed using Taq ligase for amplification (Barany (1991) Proc. Natl. Acad. Sci USA 88:189). In such cases, ligation will occur only if there is a perfect match at the 3' end of the 5' sequence making it possible to detect the presence of a known mutation at a specific site by looking for the presence or absence of amplification.
  • kits which include at least one probe nucleic acid or antibody reagent described herein, which may be conveniently used, e.g., in clinical settings to diagnose patients exhibiting symptoms or family history of a disease or illness involving a BAL gene such as non-Hodgkin's lymphoma.
  • Such kits can optionally include instructions for use.
  • any cell type or tissue in which BAL is expressed may be used in the prognostic assays described herein.
  • Monitoring the influence of agents (e.g., drugs) on the expression or activity of a BAL protein can be applied not only in basic drug screening, but also in clinical trials.
  • agents e.g., drugs
  • the effectiveness of an agent determined by a screening assay as described herein to increase BAL gene expression, protein levels, or upregulate BAL activity can be monitored in clinical trials of subjects exhibiting decreased BAL gene expression, protein levels, or downregulated BAL activity.
  • the effectiveness of an agent determined by a screening assay to decrease BAL gene expression, protein levels, or downregulate BAL activity can be monitored in clinical trials of subjects exhibiting increased BAL gene expression, protein levels, or upregulated BAL activity.
  • a BAL gene and preferably, other genes that have been implicated in, for example, a BAL-associated disorder can be used as a "read out" or markers of the phenotype of a particular cell.
  • genes, including BAL that are modulated in cells by treatment with an agent (e.g., compound, drug or small molecule) which modulates BAL activity (e.g., identified in a screening assay as described herein) can be identified.
  • cells can be isolated and RNA prepared and analyzed for the levels of expression of BAL and other genes implicated in the BAL-associated disorder, respectively.
  • the levels of gene expression e.g. , a gene expression pattern
  • the levels of gene expression can be quantified by northern blot analysis or RT-PCR, as described herein, or alternatively by measuring the amount of protein produced, by one of the methods described herein, or by measuring the levels of activity of BAL or other genes.
  • the gene expression pattern can serve as a marker, indicative of the physiological response of the cells to the agent. Accordingly, this response state may be determined before, and at various points during treatment of the individual with the agent.
  • the present invention provides a method for monitoring the effectiveness of treatment of a subject with an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate identified by the screening assays described herein) including the steps of (i) obtaining a pre-administration sample from a subject prior to administration of the agent; (ii) detecting the level of expression of a BAL protein, mRNA, or genomic DNA in the preadministration sample; (iii) obtaining one or more post-administration samples from the subject; (iv) detecting the level of expression or activity of the BAL protein, mRNA, or genomic DNA in the post-administration samples; (v) comparing the level of expression or activity of the BAL protein, mRNA, or genomic DNA in the preadministration sample with the BAL protein, mRNA, or genomic DNA in the post administration sample or samples; and (vi) altering the administration of the agent to the subject accordingly.
  • an agent e.g., an agonist
  • BAL expression or activity may be used as an indicator of the effectiveness of an agent, even in the absence of an observable phenotypic response.
  • the present invention provides for both prophylactic and therapeutic methods of treating a subject at risk of (or susceptible to) a disorder or having a disorder associated with aberrant BAL expression or activity e.g., a malignancy such as a lymphoma, e.g., non-Hodgkin's lymphoma.
  • a malignancy such as a lymphoma, e.g., non-Hodgkin's lymphoma.
  • Such treatments may be specifically tailored or modified, based on knowledge obtained from the field of pharmacogenomics.
  • “Pharmacogenomics” refers to the application of genomics technologies such as gene sequencing, statistical genetics, and gene expression analysis to drugs in clinical development and on the market.
  • the term refers the study of how a patient's genes determine his or her response to a drug (e.g., a patient's "drug response phenotype", or "drug response genotype”.)
  • a drug e.g., a patient's "drug response phenotype", or "drug response genotype”.
  • another aspect of the invention provides methods for tailoring an individual's prophylactic or therapeutic treatment with either the BAL molecules of the present invention or BAL modulators according to that individual's drug response genotype.
  • Pharmacogenomics allows a clinician or physician to target prophylactic or therapeutic treatments to patients who will most benefit from the treatment and to avoid treatment of patients who will experience toxic drug-related side effects.
  • the invention provides a method for preventing in a subject, a disease or condition associated with an aberrant BAL expression or activity, by administering to the subject a BAL molecule or an agent which modulates BAL expression or at least one BAL activity.
  • Subjects at risk for a disease which is caused or contributed to by aberrant BAL expression or activity can be identified by, for example, any or a combination of diagnostic or prognostic assays as described herein.
  • a prophylactic agent can occur prior to the manifestation of symptoms characteristic of the BAL aberrancy, such that a disease or disorder is prevented or, alternatively, delayed in its progression.
  • a BAL molecule, BAL agonist, or BAL antagonist can be used to treat the subject.
  • the appropriate agent can be determined based on, for example, the screening assays described herein.
  • the modulatory method of the invention involves contacting a cell with a BAL or agent that modulates one or more of the activities of BAL protein activity associated with the cell.
  • An agent that modulates BAL protein activity can be an agent as described herein, such as a nucleic acid or a protein, a naturally-occurring target molecule of a BAL protein (e.g., a BAL substrate), a BAL antibody, a BAL agonist or antagonist, a peptidomimetic of a BAL agonist or antagonist, or other small molecule.
  • the agent stimulates one or more BAL activities.
  • stimulatory agents include active BAL protein and a nucleic acid molecule encoding BAL that has been introduced into the cell.
  • the agent inhibits one or more BAL activities.
  • inhibitory agents include antisense BAL nucleic acid molecules, anti-BAL antibodies, and BAL inhibitors.
  • the method involves administering an agent (e.g., an agent identified by a screening assay described herein), or combination of agents that modulate (e.g., upregulate or downregulate) BAL expression or activity.
  • an agent e.g., an agent identified by a screening assay described herein
  • the method involves administering a BAL protein or nucleic acid molecule as therapy to compensate for reduced or aberrant BAL expression or activity.
  • Stimulation of BAL activity is desirable in situations in which BAL is abnormally downregulated and/or in which increased BAL activity is likely to have a beneficial effect.
  • stimulation of BAL activity is desirable in situations in which a BAL molecule is downregulated and/or in which increased BAL activity is likely to have a beneficial effect.
  • inhibition of BAL activity is desirable in situations in which BAL is abnormally upregulated and/or in which decreased BAL activity is likely to have a beneficial effect.
  • BAL molecules of the present invention as well as agents, or modulators which have a stimulatory or inhibitory effect on BAL activity (e.g., BAL gene expression) as identified by a screening assay described herein can be administered to individuals to treat (prophylactically or therapeutically) BAL-associated disorders (e.g., e.g., malignancies such as non-Hodgkin's lymphoma).
  • BAL-associated disorders e.g., e.g., malignancies such as non-Hodgkin's lymphoma
  • pharmacogenomics i.e., the study of the relationship between an individual's genotype and that individual's response to a foreign compound or drug
  • Differences in metabolism of therapeutics can lead to severe toxicity or therapeutic failure by altering the relation between dose and blood concentration of the pharmacologically active drug.
  • a physician or clinician may consider applying knowledge obtained in relevant pharmacogenomics studies in determining whether to administer a BAL molecule or BAL modulator as well as tailoring the dosage and/or therapeutic regimen of treatment with a BAL molecule or BAL modulator.
  • Pharmacogenomics deals with clinically significant hereditary variations in the response to drugs due to altered drug disposition and abnormal action in affected persons. See, for example, Eichelbaum, M. et al. (1996) Clin. Exp. Pharmacol. Physiol. 23(10-11) :983-985 and Linder, M.W. et al. (1997) Clin. Chem. 43(2):254-266.
  • two types of pharmacogenetic conditions can be differentiated. Genetic conditions transmitted as a single factor altering the way drugs act on the body (altered drug action) or genetic conditions transmitted as single factors altering the way the body acts on drugs (altered drug metabolism). These pharmacogenetic conditions can occur either as rare genetic defects or as naturally-occurring polymorphisms.
  • G6PD glucose-6-phosphate dehydrogenase deficiency
  • oxidant drugs anti-malarials, sulfonamides, analgesics, nitrofurans
  • a genome-wide association relies primarily on a high-resolution map of the human genome consisting of already known gene-related markers (e.g., a "bi- allelic” gene marker map which consists of 60,000-100,000 polymorphic or variable sites on the human genome, each of which has two variants.)
  • gene-related markers e.g., a "bi- allelic” gene marker map which consists of 60,000-100,000 polymorphic or variable sites on the human genome, each of which has two variants.
  • Such a high-resolution genetic map can be compared to a map of the genome of each of a statistically significant number of patients taking part in a Phase II/III drug trial to identify markers associated with a particular observed drug response or side effect.
  • such a high resolution map can be generated from a combination of some ten-million known single nucleotide polymorphisms (SNPs) in the human genome.
  • SNP single nucleotide polymorphisms
  • a "SNP" is a common alteration that occurs in a single nucleotide base in a stretch of DNA. For example, a SNP may occur once per every 1000 bases of DNA.
  • a SNP may be involved in a disease process, however, the vast majority may not be disease- associated.
  • individuals Given a genetic map based on the occurrence of such SNPs, individuals can be grouped into genetic categories depending on a particular pattern of SNPs in their individual genome. In such a manner, treatment regimens can be tailored to groups of genetically similar individuals, taking into account traits that may be common among such genetically similar individuals.
  • a method termed the "candidate gene approach” can be utilized to identify genes that predict drug response.
  • a gene that encodes a drugs target e.g., a BAL protein of the present invention
  • all common variants of that gene can be fairly easily identified in the population and it can be determined if having one version of the gene versus another is associated with a particular drug response.
  • the activity of drug metabolizing enzymes is a major determinant of both the intensity and duration of drug action.
  • drug metabolizing enzymes e.g., N-acetyltransferase 2 (NAT 2) and cytochrome P450 enzymes CYP2D6 and CYP2C19
  • NAT 2 N-acetyltransferase 2
  • CYP2D6 and CYP2C19 cytochrome P450 enzymes
  • CYP2D6 and CYP2C19 cytochrome P450 enzymes
  • These polymorphisms are expressed in two phenotypes in the population, the extensive metabolizer (EM) and poor metabolizer (PM). The prevalence of PM is different among different populations.
  • the gene coding for CYP2D6 is highly polymorphic and several mutations have been identified in PM, which all lead to the absence of functional CYP2D6. Poor metabolizers of CYP2D6 and CYP2C19 quite frequently experience exaggerated drug response and side effects when they receive standard doses. If a metabolite is the active therapeutic moiety, PM show no therapeutic response, as demonstrated for the analgesic effect of codeine mediated by its CYP2D6-formed metabolite morphine. The other extreme are the so called ultra-rapid metabolizers who do not respond to standard doses. Recently, the molecular basis of ultra-rapid metabolism has been identified to be due to CYP2D6 gene amplification.
  • a method termed the "gene expression profiling" can be utilized to identify genes that predict drug response.
  • a drug e.g., a BAL molecule or BAL modulator of the present invention
  • the gene expression of an animal dosed with a drug can give an indication whether gene pathways related to toxicity have been turned on.
  • Information generated from more than one of the above pharmacogenomics approaches can be used to determine appropriate dosage and treatment regimens for prophylactic or therapeutic treatment an individual. This knowledge, when applied to dosing or drug selection, can avoid adverse reactions or therapeutic failure and thus enhance therapeutic or prophylactic efficiency when treating a subject with a BAL molecule or BAL modulator, such as a modulator identified by one of the exemplary screening assays described herein.
  • Human DLB-CL cell lines DHL-4, DHL-7, DHL-8, DHL- 10, HT, and the Burkitt's cell line Namalwa were cultured in RPMI 1640 supplemented with 10% heat-inactivated fetal calf serum, 2 mM glutamine, 1 mM sodium pyruvate, 10 mM Herpes buffer and penicillin/streptomycin.
  • Cryopreserved primary tumor specimens were obtained from DLB-CL patients with known clinical prognostic characteristics and long-term follow-up. Total RNA was isolated from the cell lines and primary tumors as described in Aguiar (1999) Blood 94(7):2403-13.
  • RNA from DLB-CL cell lines and primary tumors was isolated, size-fractionated in 1% Agarose/formaldehyde gels and transferred to nylon membranes as described in Aguiar, Blood (supra). These membranes and additional multiple tissue northern blots (Clontech, Palo Alto, CA) were hybridized according to standard protocols with either a differential display fragment probe, an 800 bp BAL probe (nucleotides 900 to 1700) or B-actin.
  • the human PAC library RPCI1 (UK HGMP Resource Centre, Cambridge UK) was screened with a BAL cDNA probe according to standard protocols. DNA from positive clones was Southern blotted and re-probed with a distinct BAL probe to confirm the specificity of the clones. PAC DNAs were Biotin labeled, and hybridization of human normal metaphases performed as described in Fletcher (1998) Nature Genetics 18(l):84-7. Image analysis was performed with a cooled CCD camera (Photometries) in conjunction with an image analysis system (Oncor). A human monochromosomal somatic cell hybrid DNA panel (UK HGMP Resource Centre, Cambridge UK) was screened by PCR according to the manufacturer's instructions.
  • the abundance of BAL in a given sample was determined by comparing the intensity of the co-amplified PCR products with scanning densitometry.
  • the sensitivity of the duplex RT-PCR was determined by constructing and analyzing a standard dilutional curve. In brief, fixed amounts of BAL negative and BAL positive cell line cDNAs were added to mimic BAL losses of 10%> -100%. Upon co-amplification, the ratio of the intensity of the two bands plotted against the percentage of BAL "loss" yields a straight line and r2 value of 0.967, indicating the power of this system in detecting reduced BAL expression in the patient samples.
  • BAL-GFP green fluorescent protein
  • pEGFP-C green fluorescent protein
  • pRc/CMV untagged expression vector
  • Linearized DNA from BAL-GFP and BAL-pRc/CMV constructs were transfected by electroporation into the Namalwa B-cell lymphoma line and selected with G418 (Sigma, St Louis, MO). Thereafter, the stable BAL-GFP or GFP-only bulk transfectants were sorted to select high GFP expressing cells.
  • the pRcCMV transfectants were cloned by limiting dilution as described in Aguiar, Blood (supra). Total cell lysates, membrane, cytoplasm, and nuclear fractions from multiple BAL-GFP or GFP-only transfectants were obtained and western blots performed as described in Aguiar, Blood (supra). Rabbit polyclonal anti-GFP anti-sera (Clontech) was used for immunological detection of BAL fusion proteins. The mouse fibroblast NIH3T3 cells were seeded on glass coverslides and transfected with BAL-GFP or GFP-alone constructs by using lipofectin (Gibco).
  • BAL was expressed at higher levels in normal anti-Ig-activated splenic B- cells than in non-activated splenic B-cells (see Figure 5). For this reason, the full length BAL cDNA was cloned by probing an Ig-activated B-cell cDNA library with the 3' BAL differential display product. Several overlapping cDNA clones were identified and 5' RACE PCR (described in, for example, Ishimaru F. et al. (1995) Blood 85:3199-3207) was used to complete the full length BAL cDNA sequence.
  • BAL L 3243bp
  • BAL S 3138bp
  • Bal human cDNA two human cDNA libraries derived from anti- immunoglobulin activated splenocytes and the Raji Burkitts lymphoma cell line cloned into pCDM8 were screened to obtain additional full length Bal cDNAs.
  • the BAL human sequence was used to search the mouse EST database.
  • a 418 bp clone (Accession Number AA475710, Soares mouse mammary gland) homologous to the human sequence was identified. This sequence was used as "anchor” to several rounds of 5' and 3' RACE assays performed with mouse (Balb-c) spleen cDNA. (The sequences obtained from the EST database were used as primers).
  • the nucleotide sequence encoding the human BAL protein is shown in Figure 1 and is set forth as SEQ ID NOJ.
  • the full length protein encoded by this nucleic acid comprises about 866 amino acids and has the amino acid sequence shown in Figure 1 and set forth as SEQ ID NOJ.
  • the coding region (open reading frame) of SEQ ID NOJ is set forth as SEQ ID NOJ.
  • the nucleotide sequence encoding the mouse BAL protein is shown in Figure 2 and is set forth as SEQ ID NO:4.
  • the full length protein encoded by this nucleic acid comprises about 866 amino acids and has the amino acid sequence shown in Figure 2 and set forth as SEQ ID NO:5.
  • the coding region (open reading frame) of SEQ ID NO:4 is set forth as SEQ ID NO:6.
  • BAL transcripts were detected in the majority of organs on a multiple tissue northern blot, BAL transcripts were most abundant in lymphoid organs (spleen, lymph colon mucosa, node, fetal liver, and peripheral blood) and several additional non- hematopoietic organs (heart, skeletal muscle) (see Figure 8).
  • BAL L and BAL S were cloned into the green fluorescent protein (GFP) expression vector (pEGFP, Clontech) and transiently transfected in NIH3T3 fibroblasts. These fibroblasts were then examined by fluorescence microscopy. Fibroblasts were chosen for BAL subcellular localization because the lymphoma cell lines have scant cytoplasm, precluding optimal microscopic detection of subcellular structures. BAL S was found to localize to the nucleus (confirmed with western blotting of cellular subfractions) whereas BAL L localized in both the nucleus and the perinuclear cytoplasm.
  • GFP green fluorescent protein
  • BAL does not interact directly with the cytoskeletal network, demonstrating that BAL may either influence cellular migration in an indirect manner, or may traffic between the cytoplasm and the nucleus and directly modulate cell migration via cytoskeleton interactions following specific signals.
  • a BAL cDNA probe was used to screen a human genomic DNA PAC library (RPCIl). Genomic BAL -positive PAC clones were used to perform FISH (fluorescence in situ hybridization) on normal human metaphases. In complementary experiments, a somatic cell hybrid panel was analyzed for BAL sequences. The BAL locus was mapped to chromosome 3q21 (see Figure 9), an area of known abnormalities in multiple hematologic malignancies, including DLB-CL and other aggressive B-cell lymphomas (Cabanillas F et al. (1988) Cancer Res., 48:5557- 5564; Schouten H. et al. (1990) Blood, 75:1841 ; Monni O. et al. (1998), Genes, Chrom. & Cancer, 21 J98-307; and (Mitelman F. et al. (1997) Nat. Genet, 15:417-474).
  • FISH fluorescence in situ hybridization
  • H2AJ protein (Accession Number Q02874).
  • the human BAL protein is 26%> identical to the histone macro-H2AJ protein (Accession Number Q02874) over amino acid residues 319-485 and 22% identical over amino acid residues 160-288.
  • the human BAL nucleic acid molecule is 98% identical to the Soares pregnant uterus NbHPU Homo sapiens cDNA clone 502921 (Accession Number AA151346) over nucleotides 2528 to 3132.
  • the murine BAL protein is 26% identical to the histone macro-H2AJ protein (Accession Number Q02874) over amino acid residues 261-450 and 24% identical over amino acid residues 74-250.
  • the murine BAL nucleic acid molecule is 99% identical to the Soares 2NbMT Mus musculus cDNA clone 1446050 (Accession Number All 57103) over nucleotides 2295 to 2739.
  • the human BAL protein was aligned with the murine BAL protein using the ALIGN program (version 2.0), a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 2. The results showed a 61.5% identity between the two sequences (see Figure 3).
  • the human BAL nucleic acid molecule was aligned with the murine BAL nucleic acid molecule using the ALIGN program (version 2.0), a PAM120 weight residue table, a gap length penalty of 16 and a gap penalty of 4. The results showed a 71.7% identity between the two sequences (see Figure 4). Analysis of the predicted 819 aa human BAL protein indicates that specific regions of human BAL have partial homology to two previously characterized domains in otherwise related proteins ( Figure 7).
  • the human BAL N-terminal region (aa 136- 256 and 335-447) contains a duplicated domain of unknown function (Pfam at www.wustl.edu) which is found in the non-histone region of histone Macro H2A, non- structural polyproteins of ssRNA viruses or on its own in a family of proteins from bacteria to eukaryotes (Pehrson J.R. et al. (1999) Nucleic Acids Research 26:2837- 2842). Taken together, these data indicate that this evolutionarily conserved, as yet uncharacterized, domain is involved in an important and ubiquitous cellular process.
  • the human BAL C-terminal region (aa 508-709), is partially homologous to protein families (myosin heavy chain and cytoskeleton linkers ezrin-radixin-moesin [ERM]) (see Figure 7) which primarily govern physically integrated cellular functions such as cell migration, motility, and shape, as well as cell/cell and cell/extra-cellular matrix interactions through adhesion molecules.
  • BAL is homologous to the rod domain (filament forming properties) of alpha and beta cardiac myosin (Warrick et al. (1987) Annual Rev. Cell Biol. 3:379-421) and to the alpha-helical region of moesin, the most abundant ERM protein in lymphocytes (Bretscher (1999) Current Biology 8(l2):72l-4).
  • BAL is phosphorylated on tyrosine
  • BAL co-associates with other tyrosine phosphoproteins
  • BAL specifically co-associates with CRK-L, SHP-2, P13K or ZAP70
  • BAL is a major component of signaling pathways in lymphohematopietic cells.
  • BAL S and BAL L cDNAs are cloned into the GFP- and HA-tagged expression vectors (pEGFP, Clontech and pHM6, Boehringer) and transfected into pEGFP-BAL and MH6-BAL into DLB-CL cell lines that express the protein (DHL-7) or lack endogenous BAL expression (DHL-4). Both BAL GFP and BAL HA transfectants are evaluated in order to confirm BAL nuclear and perinuclear cytoplasmic localization in DLB-CLs. To characterize BAL function, BAL ⁇ is preferentially used because its smaller tagged protein is more likely to retain the physiologically relevant binding sites. Tyrosine Phosphorylation of BAL and Additional Co-associated Proteins
  • BAL is immunoprecipitated from untreated or anti-Ig-treated DHL-7 and DHL-4 pHM6-BAL transfectants using an HA monoclonal antibody. Thereafter, the BAL HA immunoprecipitates are immunoblotted with a phosphotyrosine antibody, 4G10 (Upstate Biotechnology, Inc.). The molecular weights of identified tyrosine phosphoproteins are compared to that of BAL and additional candidate co-associated tyrosine phosphoproteins.
  • BAL HA immunoprecipitates are blotted with specific antibodies to potential co-associating tyrosine phosphoproteins such as CRK/CRK-L, SHP-2, P13K, ZAP70 and additional candidates with molecular weights that are similar to those of identified BAL co-associated phosphoproteins. Because it may be easier to isolate co- associated proteins with concentrated highly purified recombinant BAL, the BAL GST fusion protein beads (described above) are also incubated with DHL-7 cell lysates, the BAL complexes are blotted, and resulting blots are probed with a phosphotyrosine antibody (4G 10).
  • a phosphotyrosine antibody 4G 10
  • Candidate co-associating proteins can further be identified using the yeast two- hybrid system (Matchmaker Two-Hybrid System by Clontech) as described in Frederickson, R. (1998) Curr. Opin. Biotechnol, 9:90-96).
  • BAL's potential effects on the local growth and distant metastasis of DLB-CL cell lines are further determined in an in vivo murine model.
  • the above-mentioned pRc-CMV brief, parental, vector-only, pRc-CMV-BAL s and BAL L DLB-CL transfectants are injected subcutaneously or via tail vein into cohorts of SCID mice.
  • Antisense BAL constructs can also be used because, as described herein, endogenous BAL is upregulated when the suspension DLB-CL cell lines form local tumors in vivo (see Figure 6).
  • a semi-quantitative duplex RT-PCR assay (as described in Aguiar, R. et al. (1997) Blood 90 (Suppl. l):491a and Aguiar, R. et al. (1997) Leukemia, 11 J33-238) was performed to access BAL expression in a large series of primary DLB-CLs. Briefly, the "target sequence” (BAL) was co-amplified with the constitutively expressed "control" ABL gene. The PCR products were size-fractionated, blotted and hybridized with internal BAL and ABL oligonucleotides.
  • the BAL cDNA was cloned into the pGEX expression vector (GST Gene Fusion System, Pharmacia). After sequencing the construct to ensure that the fusion was in frame and that no mutations had been introduced in the BAL sequence, bacterial cultures containing pGEX-BAL were treated with IPTG (isopropyl-1-Thio-b-D-Galactopyearanoside) and the GST-Bal fusion protein was induced and affinity-purified on gluthathione-S-agarose beads. Balb-c mice are immunized with the affinity-purified GST-BAL protein and their spleens harvested for generation of BAL monoclonal antibodies.
  • GST Gene Fusion System GST Gene Fusion System, Pharmacia
  • Monoclonal antibodies are initially screened for reactivity with pGEX-BAL and not with pGEX alone using ELISA. Positive hybridoma supernatants are then screened against immunoblotted parental and BAL DLB-CL transfectants for reactivity with the appropriate-sized BAL protein.
  • Immunoperoxidase staining of primary tumor specimens from a large series of well-characterized DLB-CL patients can also be performed using the BAL monoclonal antibody produced as described above.
  • BAL maps to chromosome band 3q21, a region which is frequently associated with non-random abnormalities (gain, loss and translocations) in NHLs (Cabanillas F et al. (1988) Cancer Res., 48:5557-5564); (Schouten H. et al. (1990) Blood, 75:1841); (Monni O. et al. (1998), Genes, Chrom. & Cancer, 21 J98-307); and (Mitelman F. et al. (1997) Nat. Genet, 15:417-474).
  • the integrity of the BAL locus is assessed in informative samples.
  • the patient's metaphases are initially probed with PAC clones encompassing the BAL locus using the FISH technique (Aguiar, R. et al. (1997) Blood, 90:3130-3135; Carapeti, M. et al. (1998) Blood, 91 :3127-3133; Aguiar, R. et al. (1997) Genes, Chrom. & Cancer, 20:408-411).
  • FISH FISH
  • BAL S was cloned into a GFP vector (pEGFP) and an untagged expression vector (pRc-CMV) and pEGFP-BAL s , pRc-CMV BAL, and vector only transfectants were generated in an aggressive lymphoma cell line that constitutively expresses low levels of BAL (see Figure 13).
  • pEGFP GFP vector
  • pRc-CMV untagged expression vector
  • pEGFP-BAL s pEGFP-BAL s
  • pRc-CMV BAL vector only transfectants were generated in an aggressive lymphoma cell line that constitutively expresses low levels of BAL
  • BAL S -GFP or GFP-only transfectants were plated in the upper chamber and analyzed for migration to the lower chamber in the presence of the hematopoietic chemoattractant factor, stromal derived factor 1- ⁇ (SDF-l ⁇ ) (see Figure 14).
  • aggressive lymphoma BAL S -GFP transfectants migrated at a 2-4 times higher rate than the GFP-alone transfectants (p ⁇ 0.01) (see Figure 14).
  • Similar results were obtained with multiple BAL s pRcCMV transfectants indicating that the GFP moiety did not affect BAL function or the observed results. Taken together, these data indicate that BAL overexpression increases the migration of an aggressive NHL cell line.
  • BAL is expressed as a recombinant glutathione-S-transferase (GST) fusion polypeptide in E. coli and the fusion polypeptide is isolated and characterized.
  • GST glutathione-S-transferase
  • BAL is fused to GST and this fusion polypeptide is expressed in E. coli, e.g., strain PEB199.
  • Expression of the GST-BAL fusion protein in PEB199 is induced with IPTG.
  • the recombinant fusion polypeptide is purified from crude bacterial lysates of the induced PEB199 strain by affinity chromatography on glutathione beads. Using polyacrylamide gel electrophoretic analysis of the polypeptide purified from the bacterial lysates, the molecular weight of the resultant fusion polypeptide is determined.
  • the pcDNA/Amp vector by Invitrogen Corporation (San Diego, CA) is used.
  • This vector contains an SV40 origin of replication, an ampicillin resistance gene, an E. coli replication origin, a CMV promoter followed by a polylinker region, and an SV40 intron and polyadenylation site.
  • a DNA fragment encoding the entire BAL protein and an HA tag (Wilson et al. (1984) Cell 37:767) or a FLAG tag fused in-frame to its 3' end of the fragment is cloned into the polylinker region of the vector, thereby placing the expression of the recombinant protein under the control of the CMV promoter.
  • the BAL DNA sequence is amplified by PCR using two primers.
  • the 5' primer contains the restriction site of interest followed by approximately twenty nucleotides of the BAL coding sequence starting from the initiation codon; the 3' end sequence contains complementary sequences to the other restriction site of interest, a translation stop codon, the HA tag or FLAG tag and the last 20 nucleotides of the BAL coding sequence.
  • the PCR amplified fragment and the pCDNA/Amp vector are digested with the appropriate restriction enzymes and the vector is dephosphorylated using the CIAP enzyme (New England Biolabs, Beverly, MA).
  • the two restriction sites chosen are different so that the BAL gene is inserted in the correct orientation.
  • the ligation mixture is transformed into E. coli cells (strains HB101, DH5a, SURE, available from Stratagene Cloning Systems, La Jolla, CA, can be used), the transformed culture is plated on ampicillin media plates, and resistant colonies are selected. Plasmid DNA is isolated from transformants and examined by restriction analysis for the presence of the correct fragment. COS cells are subsequently transfected with the BAL-pcDNA/Amp plasmid
  • DNA using the calcium phosphate or calcium chloride co-precipitation methods, DEAE- dextran-mediated transfection, lipofection, or electroporation.
  • Other suitable methods for transfecting host cells can be found in Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989.
  • the expression of the BAL polypeptide is detected by radiolabelling ( 35 S-methionine or 35 S-cysteine available from NEN, Boston, MA, can be used) and immunoprecipitation (Harlow, E. and Lane, D.
  • HA specific monoclonal antibody A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1988
  • the cells are labelled for 8 hours with 35 S-methionine (or 35 S-cysteine).
  • the culture media are then collected and the cells are lysed using detergents (RIPA buffer, 150 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% DOC, 50 mM Tris, pH 7.5). Both the cell lysate and the culture media are precipitated with an HA specific monoclonal antibody. Precipitated polypeptides are then analyzed by SDS-PAGE.
  • DNA containing the BAL coding sequence is cloned directly into the polylinker of the pCDNA/Amp vector using the appropriate restriction sites.
  • the resulting plasmid is transfected into COS cells in the manner described above, and the expression of the BAL polypeptide is detected by radiolabelling and immunoprecipitation using a BAL specific monoclonal antibody.

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Abstract

L'invention concerne des molécules isolées d'acides nucléiques désignées molécules d'acides nucléiques BAL et exprimées différemment dans le lymphome autre que le lymphome de Hodgkin. Elle concerne également des molécules d'acides nucléiques antisens, des vecteurs d'expression de recombinaison contenant des molécules d'acides nucléiques BAL, des cellules hôtes dans lesquelles les vecteurs d'expression ont été introduits et des animaux transgéniques non humains dans lesquels un gène de BAL a été introduit ou dissocié. Elle concerne, de plus, des protéines isolées de BAL, des protéines de fusion, des peptides antigéniques et des anticorps anti-BAL. Elle concerne enfin des méthodes diagnostiques mettant en application les compositions décrites par l'invention.
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Title
DATABASE EMBL [Online] 1 October 1998 (1998-10-01), "ud16c02.r1 Soares 2NbMT Mus musculus cDNA clone IMAGE:1446050 5', mRNA sequence." XP002316476 retrieved from EBI accession no. EM_EST:AI157103 Database accession no. AI157103 *
DATABASE EMBL [Online] 14 December 1996 (1996-12-14), "mr05c07.r1 Soares mouse 3NbMS Mus musculus cDNA clone IMAGE:596556 5', mRNA sequence." XP002316475 retrieved from EBI accession no. EM_EST:MMAA46363 Database accession no. MMAA46363 *
DATABASE EMBL [Online] 15 December 1996 (1996-12-15), "zl25b01.r1 Soares_pregnant_uterus_NbHPU Homo sapiens cDNA clone IMAGE:502921 5', mRNA sequence." XP002316478 retrieved from EBI accession no. EM_EST:HSAA51346 Database accession no. HSAA51346 *
DATABASE EMBL [Online] 22 September 1998 (1998-09-22), "qc34a12.x1 Soares_pregnant_uterus_NbHPU Homo sapiens cDNA clone IMAGE:1711486 3', mRNA sequence." XP002316477 retrieved from EBI accession no. EM_EST:AI129360 Database accession no. AI129360 *
DATABASE EMBL [Online] 25 April 1998 (1998-04-25), "AF046630 Mus musculus 129Sv/Ev Mus musculus genomic clone OST8563, DNA sequence." XP002316474 retrieved from EBI accession no. EM_GSS:AF046630 Database accession no. AF046630 & ZAMBROWICZ ET AL.: NATURE, vol. 392, 1998, pages 608-611, *
See also references of WO0026231A1 *
YAKUSHIJIN Y ET AL: "Molecular characterization of a novel gene, bal, which regulates the proliferation of aggressive B-cell lymphomas" BLOOD, vol. 90, no. 10 SUPPL. 1 PART 1, 15 November 1997 (1997-11-15), page 177A, XP008042576 & 39TH ANNUAL MEETING OF THE AMERICAN SOCIETY OF HEMATOLOGY; SAN DIEGO, CALIFORNIA, USA; DECEMBER 5-9, 1997 ISSN: 0006-4971 *

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