ANAPLASTIC LYMPHOMA KINASE CHIMERIC ANTIGEN RECEPTORS AND METHODS OF USE

BACKGROUND OF THE INVENTION

Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase in the insulin receptor superfamily, which plays an important role in the development of the brain and nervous system. ALK is processed into peptides by the proteasome, transported to the endoplasmic reticulum by transporters associated with antigen processing-1 and -2 (TAP1 and TAP2), and binds to the HLA class I molecules. ALK is minimally expressed by normal tissues during adulthood. However, ALK is aberrantly expressed by tumors, such as non-small cell lung cancer (NSCLC), anaplastic large cell lymphoma (ALCL), and neuroblastoma. More rarely, ALK is expressed by B-cell lymphoma, thyroid cancer, colon cancer, breast cancer, inflammatory myofibroblastic tumors (IMT), renal carcinoma, esophageal cancer, and melanoma. Thus, ALK is an ideal shared antigen across different type of cancers. ALK may become oncogenic by forming a fusion gene with other genes, by gaining additional gene copies, or by genetic mutations.

Several ALK tyrosine kinase inhibitors (TKIs) are available for the treatment of ALK-rearranged NSCLC, including crizotinib, ceritinib, alectinib, brigatinib, and lorlatinib. Unfortunately, resistance to these drugs occurs within 1-2 years through a variety of mechanisms. Once patients develop resistance to available ALK inhibitors, they are typically treated with cytotoxic chemotherapy rather than immunotherapy since response rates to PD-1 pathway inhibitors in this population are very low. Although PD-1 inhibitors such as pembrolizumab (Keytruda®) and nivolumab (Opdivo®) have revolutionized the treatment of lung cancer in general, particularly in smoking-associated cancers, most patients with ALK-positive lung cancer do not respond to these immunotherapies. Thus, the development of additional ALK-targeted therapy in ALK-positive cancers is clearly a need.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. Absent any indication otherwise, publications, patents, and patent applications mentioned in this specification are incorporated herein by reference in their entireties

SUMMARY OF THE INVENTION

As described below, the present invention features anaplastic lymphoma kinase chimeric antigen receptors (ALK CARs). The invention also provides engineered immune cells comprising an ALK CAR, polynucleotides encoding ALK CARs, pharmaceutical compositions thereof, and kits for administering the same. Methods of treating a subject with a disease by administering the ALK CAR, engineered immune cell comprising an ALK CAR, or polynucleotides encoding ALK CARs, or pharmaceutical compositions thereof, are also provided.

One aspect of the invention provides an anaplastic lymphoma kinase chimeric antigen receptor (ALK CAR) comprising: an extracellular binding domain comprising a heavy chain complementarity determining region 1 (HCDR1), a heavy chain complementarity determining region 2 (HCDR2), and a heavy chain complementarity determining region 3 (HCDR3) each comprising an amino acid sequence that is at least 80% identical to the HCDR1, HCDR2, and HCDR3 sequences of an anti-ALK antibody in Table 4, wherein the extracellular binding domain specifically binds to an anaplastic lymphoma kinase (ALK) polypeptide or antibody-binding fragment thereof; a transmembrane domain; and at least one signaling domain.

In some embodiments, the extracellular binding domain comprises the HCDR1, HCDR2, and HCDR3 amino acid sequences of an anti-ALK antibody in Table 4. In some embodiments, the extracellular binding domain further comprising a light chain complementarity determining region 1 (LCDR1), a light chain complementarity determining region 2 (LCDR2), and a light chain complementarity determining region 3 (LCDR3) each comprising an amino acid sequence that is at least 80% identical to the LCDR1, LCDR2 and LCDR3 sequences of an anti-ALK antibody in Table 3. In some embodiments, the extracellular binding domain comprises the LCDR1, LCDR2 and LCDR3 amino acid sequences of an anti-ALK antibody in Table 3.

In another aspect, the invention provides an anaplastic lymphoma kinase chimeric antigen receptor (ALK CAR) comprising: an extracellular binding domain comprising a heavy chain variable region (VH) comprising an amino acid sequence that is at least 80% identical to the VH of an anti-ALK antibody in Table 2, wherein the extracellular binding domain specifically binds to an anaplastic lymphoma kinase (ALK) polypeptide or antibody-binding fragment thereof; and a transmembrane domain; and at least one signaling domain.

In some embodiments, the extracellular binding domain comprises the VH of an anti-ALK antibody in Table 2. In some embodiments, the extracellular binding domain further comprises a light chain variable region (VL) comprising an amino acid sequence that is at least 80% identical to the VL of an anti-ALK antibody in Table 1. In some embodiments, the extracellular binding domain comprises the VL of an anti-ALK antibody in Table 1. In some embodiments, the VH comprises human framework regions. In some embodiments, the VL comprises human framework regions.

In some embodiments, the ALK CAR includes a linker. In one embodiment, the linker is a flexible peptide linker. In one embodiment, the linker is (Gly₄Ser)_n. In some embodiments, the ALK CAR includes a reporter gene. In one embodiment, the reporter gene is green fluorescent protein (GFP). In some embodiments, the extracellular binding domain is an scFv.

In some embodiments, the anti-ALK antibody comprises VH CDR amino acid sequences SYWMN, QIYPGDGDTNYNGKFKG, and YYYGSKAY, and VL CDR amino acid sequences RASENIYYSLA, NANSLED, KQAYDVPFT.

In some embodiments, the anti-ALK antibody comprises VH CDR amino acid sequences SYWMH, RIDPNSGGTKYNEKFKS, and DYYGSSYRFAY, and VL CDR amino acid sequences SVSQGISNSLN, YTSSLHS, and QQYSKLPLT.

In some embodiments, the anti-ALK antibody comprises VH CDR amino acid sequences NYWMH, YINPSSGYTKYNQKFKD, and DYYGSSSWFAY, and VL CDR amino acid sequences KASQNVGTNVA, SASYRYS, and QQYNSYPYMYT.

In some embodiments, the anti-ALK antibody comprises VH CDR amino acid sequences SYWVN, QIYPGDGDTNYNGKFKG, and SRGYFYGSTYDS, and VL CDR amino acid sequences RASESVDNYGISFMN, AASNQGS, and QQSKEVPWT.

In some embodiments, the anti-ALK antibody comprises VH CDR amino acid sequences SYWMH, YIKPSSGYTKYNQKFKD, and DYYGSSSWFAY, and VL CDR amino acid sequences KASQNVGTNVA, SASYRYS, and QQYNSYPYMYT.

In some embodiments, the anti-ALK antibody comprises VH CDR amino acid sequences SYAMS, YISSGGDYIYYADTVKG, and ERIWLRRFFDV, and VL CDR amino acid sequences KASQNVGTAVA, SASNRFT, and QQYSSYPLT.

In some embodiments, the anti-ALK antibody comprises VH CDR amino acid sequences SYWMH, YINPSSGYTKYNQKFKD, and DYYGSSSWFAY, and VL CDR amino acid sequences KASQNVGTNVA, SASYRYS, and QRYNSYPYMFT.

In some embodiments, the anti-ALK antibody comprises VH amino acid sequence QVQLQQSGAELVKPGASVKISCKASGYAFSSYWMNWVKQRPGKGLEWIGQIYPGDGD TNYNGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCASYYYGSKAYWGQGTLVT VSA, and VL amino acid sequence DIQMTQSPASLAASVGETVTITCRASENIYYSLAWYQQKQGKSPQLLIYNANSLEDGVPS RFSGSGSGTQYSMKINSMQPEDTATYFCKQAYDVPFTFGSGTKLEIKR

In some embodiments, the anti-ALK antibody comprises VH amino acid sequence QVQLQQPGAEFVKPGASVKLSCKASGYTFTSYWMIHWVKQRPGRGLEWIGRIDPNSGG TKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARDYYGSSYRFAYWGQGTL VTVSA, and VL amino acid sequence AIQMTQTTSSLSASLGDRVTISCSVSQGISNSLNWYQQKPDGTVKLLIYYTSSLHSGVPSR FSGSGSGTDYSLTISNLEPEDIATYYCQQYSKLPLTFGAGTKLELKR.

In some embodiments, the anti-ALK antibody comprises VH amino acid sequence QVQLQQSGAELAKPGASVKLSCKASGYTFTNYWMHWVKQRPGQGLEWIGYINPSSGY TKYNQKFKDKATLTADKSSSTAYMQLSSLTYEDSAVYYCARDYYGSSSWFAYWGQGT LVTVSA, and VL amino acid sequence DIVMTQSQRFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKALIYSASYRYSGV PDRFTGSGSGTDFTLTVSNVQSEDLAEYFCQQYNSYPYMYTFGGGTKLEIKR.

In some embodiments, the anti-ALK antibody comprises VH amino acid sequence QVQLQQSGAELVKPGASVKISCKASGYAFSSYWVNWVKQRPGKGLEWIGQIYPGDGDT NYNGKFKGKATLTADKSSSTAYMQLSSLTSEDSAVYFCARSRGYFYGSTYDSWGQGTT LTVSS, and VL amino acid sequence DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFMNWFQQKPGQPPKLLIYAASNQGS GVPARFSGSGSGTDFSLNIHPMEEDDTAMYFCQQSKEVPWTFGGGTKLEIKR.

In some embodiments, the anti-ALK antibody comprises VH amino acid sequence QVQLQQSGAELAKPGASVKLSCKASGYTFTSYWMHWVKQRPGQGLEWIGYIKPSSGY TKYNQKFKDKATLTADKSSSTAYMQLSSLTYEDSAVYYCARDYYGSSSWFAYWGQGT

LVTVSA, and VL amino acid sequence DIVMTQSQRFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKALIYSASYRYSGV PDRFTGSGSGTDFTLTISNVQSEDLAEYFCQQYNSYPYMYTFGGGTKLEIKR.

In some embodiments, the anti-ALK antibody comprises VH amino acid sequence DVKLVESGEGLVKPGGSLKLSCAASGFTFSSYAMSWVRQTPEKRLEWVTYISSGGDYIY YADTVKGRFTISRDNARNTLYLQMSSLKSEDTAMYYCTRERIWLRRFFDVWGTGTTVT VSS, and VL amino acid sequence DIVMTQSQKFMSTSVGDRVSITCKASQNVGTAVAWYQLKPGQSPKLLIYSASNRFTGVP DRFTGSGSGTDFTLTISNMQSEDLADYFCQQYSSYPLTFGSGTKLEIKR.

In some embodiments, the anti-ALK antibody comprises VH amino acid sequence QVQLQQSGAELAKPGASVKLSCKASGYTFTSYWMHWVKQRPGQGLEWIGYINPSSGY TKYNQKFKDKATLTADKSSSTAYMQLSSLTFEDSAVYYCARDYYGSSSWFAYWGQGT LVTVSA, and VL amino acid sequence DIVMTQSQKFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGHSPKALIYSASYRYSGV PDRFTGSGSGTDFTLTISNVQSEDLAEYFCQRYNSYPYMFTFGGGTKLEIKR.

In some embodiments, the transmembrane domain is selected from the group consisting of CD8, CD137 (4-1BB), and CD28 in one embodiment, the transmembrane domain is CD8. In some embodiments, the at least one signaling domain is selected from the group consisting of CD8, CD28, CD134 (OX40), CD137 (4-1BB), and CD3ζ. In one embodiment, the at least one signaling domain is CD28 and CD3ζ.

In some embodiments, the structure of the ALK CAR from 5′ to 3′ includes: the extracellular binding domain, a CD8 transmembrane domain, a CD28 signaling domain, and a CD3ζ signaling domain. In some embodiments, the ALK CAR includes a signal peptide. In one embodiment, the signal peptide is mCD8, CD8α, or GM-CSF. In some embodiments, the ALK

CAR includes a splice donor and/or splice acceptor site. In some embodiments, the ALK CAR includes a packaging signal. In some embodiments, the ALK CAR includes the backbone structure and domains of the m1928z CAR. In some embodiments, the extracellular binding domain specifically binds to an extracellular domain of an anaplastic lymphoma kinase (ALK) polypeptide or antibody-binding fragment thereof.

One aspect of the invention provides a polynucleotide encoding an ALK CAR as provided herein.

In another aspect, the invention provides a vector comprising a polynucleotide as provided herein. In some embodiments, the vector is a viral vector. In some embodiments, the vector is a lentiviral, a retroviral, an adenoviral, an Adeno-Associated Virus (AAV), a plasmid, a transposon, and insertion sequence, or an artificial chromosomal vector. In some embodiments, the vector includes a promoter operably linked to the polynucleotide sequence encoding the ALK CAR.

One aspect of the invention provides an engineered immune cell expressing at the cell surface membrane an ALK CAR as provided herein.

In another aspect, the invention provides an engineered immune cell produced by transforming an immune cell with a polynucleotide as provided herein or transducing with a vector as provided herein. In some embodiments, the engineered immune cell is derived from inflammatory T-lymphocytes, cytotoxic T-lymphocytes, regulatory T-lymphocytes, natural killer T (NKT) cells, natural killer (NK) cells, or helper T-lymphocytes. In some embodiments, the engineered immune cell further expresses one or more cytokines. In some embodiments, the cytokine is selected from the group consisting of: interleukin-1 (IL-1), interleukin-2 (IL-2), interleukin-4 (IL-4), interleukin-6 (IL-6), interleukin-7 (IL-7), interleukin-12 (IL-12), interleukin-15 (IL-15), interleukin-21 (IL-21), the protein memory T-cell attractant “Regulated on Activation, Normal Expressed and Secreted” (RANTES), granulocyte-macrophage-colony stimulating factor (GM-CSF), tumor necrosis factor-alpha (TNF-α), or interferon-gamma (IFN-γ), and macrophage inflammatory protein 1 alpha (MIP-1α). In one embodiment, the cytokine is a human cytokine.

In some embodiments, the engineered immune cell is for use in the treatment of an ALK-positive cancer. In some embodiments, the ALK-positive cancer is selected from the group consisting of non-small cell lung cancer (NSCLC), anaplastic large cell lymphoma (ALCL), neuroblastoma, B-cell lymphoma, thyroid cancer, colon cancer, breast cancer, inflammatory myofibroblastic tumors (IMT), renal carcinoma, esophageal cancer, and melanoma. In one embodiment, the ALK-positive cancer is neuroblastoma or melanoma. In another embodiment, the ALK-positive cancer is neuroblastoma. In another embodiment, the ALK-positive cancer is melanoma. In some embodiments, the ALK-positive cancer has an ALK^F1174Lactivating point mutation.

One aspect of the invention provides a method of engineering an immune cell comprising: providing an immune cell; and expressing at the surface of the immune cell at least one ALK CAR as provided herein.

In another aspect, the invention provides a method of engineering an immune cell comprising: providing an immune cell; introducing into the immune cell a polynucleotide as provided herein; and expressing the polynucleotide in the immune cell. In some embodiments, the immune cell is isolated from a subject. In some embodiments, the immune cell is selected from an inflammatory T-lymphocyte, cytotoxic T-lymphocyte, regulatory T-lymphocyte, natural killer T (NKT) cell, natural killer (NK) cell, or helper T-lymphocyte.

One aspect of the invention provides a pharmaceutical composition comprising an ALK CAR as provided herein, a polynucleotide as provided herein, or an engineered immune as provided herein, and a pharmaceutically acceptable carrier, diluent, or excipient. In some embodiments, the composition comprises an effective amount of a ALK CAR as provided herein, a polynucleotide as provided herein, or an engineered immune cell as provided herein.

In another aspect, the invention provides a method of treating a subject with an ALK-positive cancer comprising administrating a pharmaceutical composition as provided herein to the subject.

In yet another aspect, the invention provides a method of treating a subject with an ALK-positive cancer comprising administering to the subject an ALK CAR as provided herein, a polynucleotide as provided herein, or an engineered immune cell as provided herein.

In another aspect, the invention provides a method of treating a subject with an ALK-positive cancer, the method comprising: transforming immune cells with a vector as provided herein to obtain an engineered immune cell, wherein the immune cell comprises a polynucleotide as provided herein; and administering an effective amount of the engineered immune cell to the subject. In some embodiments, the immune cells are derived from the subject. In some embodiments, the immune cells are derived from a donor. In some embodiments, the method includes administering an effective amount of an ALK vaccine to the subject, wherein the ALK vaccine comprises at least one isolated ALK polypeptide or polynucleotide.

One aspect of the invention provides a method of treating a subject with an ALK-positive cancer, the method comprising administering an effective amount of an engineered immune cell comprising an ALK CAR and an effective amount of an ALK vaccine comprising at least one isolated ALK polypeptide or polynucleotide to the subject. In some embodiments, the engineered immune cell is administered simultaneously or sequentially with the ALK vaccine to the subject. In some embodiments, the ALK polypeptide or polynucleotide is conjugated to an amphiphile. In one embodiment, the amphiphile is N-hydroxy succinimidyl ester-end-functionalized poly(ethylene glycol)-lipid (NHS-PEG2KDa-DSPE). In some embodiments, the method includes administering, simultaneously or sequentially, an effective amount of one or more of an ALK inhibitor, immune checkpoint inhibitor, and/or tyrosine kinase inhibitor (TKI). In some embodiments, the method includes administering, simultaneously or sequentially, an effective amount of a tyrosine kinase inhibitor (TKI). In one embodiment, the TKI is lorlatinib. In some embodiments, the method includes administering, simultaneously or sequentially, an effective amount of an immunosuppressor. In one embodiment, the immunosuppressor is cyclophosphamide (CTX).

In some embodiments, the subject is a mammal. In some embodiments, the subject is a human or rodent. In some embodiments, the ALK-positive cancer is selected from the group consisting of non-small cell lung cancer (NSCLC), anaplastic large cell lymphoma (ALCL), neuroblastoma, B-cell lymphoma, thyroid cancer, colon cancer, breast cancer, inflammatory myofibroblastic tumors (IMT), renal carcinoma, esophageal cancer, and melanoma. In some embodiments, the ALK-positive cancer is neuroblastoma or melanoma. In one embodiment, the ALK-positive cancer has an ALK^F1174Lactivating point mutation.

One aspect of the invention provides a kit comprising an agent for administration to a subject. In some embodiments, the agent is an ALK CAR as provided herein, a polynucleotide as provided herein, an engineered immune cell as provided herein, a pharmaceutical composition as provided herein, or a vector as provided herein. In some embodiments, the kit includes instructions for using the kit.

Compositions and articles defined by the invention were isolated or otherwise manufactured in connection with the examples provided below. Other features and advantages of the invention will be apparent from the detailed description, and from the claims.

Definitions

Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person skilled in the art to which this invention pertains or relates. The following references provide one of skill with a general definition of many of the terms used in this invention: Singleton et al., Dictionary of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge Dictionary of Science and Technology (Walker ed., 1988); The Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer Verlag (1991); Benjamin Lewin, Genes V, published by Oxford University Press, 1994 (ISBN 0-19-854287-9); Kendrew et al. (eds.); The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); Molecular Biology and Biotechnology: a Comprehensive Desk Reference, Robert A. Meyers (ed.), published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8); and Hale & Marham, The Harper Collins Dictionary of Biology (1991). As used herein, the following terms have the meanings ascribed to them below, unless specified otherwise.

By “adjuvant” is meant a substance or vehicle that non-specifically enhances the immune response to an antigen. Adjuvants may include a suspension of minerals (e.g., alum, aluminum hydroxide, or phosphate) on which antigen is adsorbed; or water-in-oil emulsion in which antigen solution is emulsified in mineral oil (e.g., Freund's incomplete adjuvant), sometimes with the inclusion of killed mycobacteria (Freund's complete adjuvant) to further enhance antigenicity. Immunostimulatory oligonucleotides (such as those including a CpG motif) can also be used as adjuvants (see, e.g., U.S. Pat. Nos. 6,194,388; 6,207,646; 6,214,806; 6,218,371; 6,239,116; 6,339,068; 6,406,705; and 6,429,199). Adjuvants also include biological molecules, such as costimulatory molecules. In some embodiments, biological adjuvants include cytokines. Exemplary biological adjuvants include, without limitation, interleukin-1 (IL-2), the protein memory T-cell attractant “Regulated on Activation, Normal T Expressed and Secreted” (RANTES), granulocyte-macrophage-colony stimulating factor (GM-CSF), tumor necrosis factor-alpha (TNF-α), interferon-gamma (IFN-γ), granulocyte-colony stimulation factor (G-CSF), lymphocyte function-associated antigen 3 (LFA-3, also called CD58), cluster of differentiation antigen 72 (CD72), (a negative regulator of B-cell responsiveness), peripheral membrane protein, B7-1 (B7-1, also called CD80), peripheral membrane protein, B7-2 (B7-2, also called CD86), the TNF ligand superfamily member 4 ligand (OX40L) or the type 2 transmembrane glycoprotein receptor belonging to the TNF superfamily (4-1BBL). In some embodiments, the adjuvant may be conjugated to an amphiphile as described in H. Liu et al., Structure-based programming of lymph-node targeting in molecular vaccines. Nature 507, 5199522 (2014). In some embodiments, the amphiphile conjugated to the adjuvant is N-hydroxy succinimidyl ester-end-functionalized poly(ethylene glycol)-lipid (NHS-PEG2KDa-DSPE).

By “administer” is meant giving, supplying, or dispensing a composition, agent, therapeutic and the like to a subject, or applying or bringing the composition and the like into contact with the subject. Administering or administration may be accomplished by any of a number of routes, such as, for example, without limitation, topical, oral, subcutaneous, intramuscular, intraperitoneal, intravenous (IV), injection, intrathecal, intramuscular, dermal, intradermal, intracranial, inhalation, rectal, intravaginal, or intraocular.

By “adoptive cell transfer” or “ACT” is meant a process in which immune effector cells (e.g. T cells) are isolated and engineered to recognize a specific antigen (i.e., “engineered immune cells”), then expanded and reintroduced to a subject. Immune effector cells (e.g., T cells) used for ACT may be “autologous,” derived from the subject to be treated, or “allogeneic” (sometimes called “homologous”), derived from a donor subject with an immunogenic profile similar enough not to be rejected by the subject receiving ACT. In some embodiments, cells to be transferred in ACT are CAR-T cells.

By “agent” is meant any small molecule chemical compound, antibody, nucleic acid molecule, peptide, polypeptide, or fragments thereof.

By “anaplastic lymphoma kinase” or “ALK” is meant a receptor tyrosine kinase belonging to the insulin receptor superfamily.

By “ALK antibody” or “anti-ALK antibody” is meant an antibody or an antigen-binding portion thereof that specifically binds to an ALK polypeptide. In some embodiments, the anti-ALK antibody binds to a murine ALK protein or an antibody-binding portion thereof. In some embodiments, the anti-ALK antibody binds to a human ALK protein or an antibody-binding portion thereof. In some embodiments, the anti-ALK antibody binds to a portion of the extracellular domain of the ALK receptor. In some embodiments, the anti-ALK antibody binds to a portion of the extracellular domain of a murine ALK receptor. In some embodiments, the anti-ALK antibody binds to a portion of the extracellular domain of a human ALK receptor. In some embodiments, the anti-ALK antibody is a murine antibody. In some embodiments, the anti-ALK antibody is a human antibody. In some embodiments, the anti-ALK antibody is a humanized antibody. In some embodiments, the anti-ALK antibody is a chimeric antibody. In some embodiments, the anti-ALK antibody modulates ALK activity (e.g., ALK signaling) and/or ALK expression.

In some embodiments, the anti-ALK antibody is an antibody selected from ALK Antibody #1 (ALK #1), ALK Antibody #2 (ALK #2), ALK Antibody #3 (ALK #3), ALK Antibody #4 (ALK #4), ALK Antibody #5 (ALK #5), ALK Antibody #6 (ALK #6), or ALK Antibody #7 (ALK #7). In some embodiments, the anti-ALK antibody is ALK #1. In some embodiments, the anti-ALK antibody is ALK #2. In some embodiments, the anti-ALK antibody is ALK #3. In some embodiments, the anti-ALK antibody is ALK #4. In some embodiments, the anti-ALK antibody is ALK #5. In some embodiments, the anti-ALK antibody is ALK #6. In some embodiments, the anti-ALK antibody is ALK #7.

By “ALK inhibitor” is meant an agent that that inhibits or decreases ALK activity, such as ALK tyrosine kinase activity. In some embodiments, an ALK inhibitor can be a small molecule, a protein (e.g., an antibody), or a nucleic acid (e.g., an antisense molecule). An ALK inhibitor may inhibit or decrease binding of a ligand (e.g., pleiotrophin) to ALK and thus decrease ALK tyrosine kinase activity. An ALK inhibitor may also directly inhibit or decrease ALK tyrosine kinase activity, for example, an ATP-competitive inhibitor (e.g., crizotinib). Molecules that decrease or inhibit expression of ALK (e.g., antisense molecules) are also ALK inhibitors. The ALK inhibitor may specifically inhibit ALK tyrosine kinase activity or may inhibit other receptor tyrosine kinase activity (e.g., c-Met/HGFR activity), in addition to inhibiting ALK tyrosine kinase activity. Nonlimiting examples of ALK inhibitors include the following: crizotinib, ceritinib, alectinib, brigatinib, and lorlatinib. PKIs or other agents that affect ALK may render ALK-positive cancers more susceptible to immune targeting with anti-ALK antibody or with CAR-expressing T cells specific for ALK.

By “ALK polypeptide,” “ALK peptide” or “ALK protein” is meant an anaplastic lymphoma kinase (ALK) protein or fragment thereof. The full-length ALK protein includes an extracellular domain, a hydrophobic stretch corresponding to a single pass transmembrane region, and an intracellular kinase domain. In some embodiments, the ALK polypeptide is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to a full-length ALK protein. In some embodiments, the ALK polypeptide is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to a full-length ALK protein in Homo Sapiens. In some embodiments, the ALK polypeptide is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to a full-length murine ALK protein. In some embodiments, the ALK polypeptide comprises an ALK extracellular domain. In some embodiments, the ALK polypeptide is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to an ALK extracellular domain in Homo Sapiens. In some embodiments, the ALK polypeptide is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to a murine ALK extracellular domain. In some embodiments, the ALK polypeptide comprises an ALK intracellular domain. In some embodiments, the ALK polypeptide is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to an ALK intracellular domain in Homo Sapiens. In some embodiments, the ALK polypeptide is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to a murine ALK intracellular domain.

In some embodiments, the ALK polypeptide comprises an amino acid sequence that is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to an ALK amino acid sequence associated with GenBank™ Accession NOs.: BAD92714.1, ACY79563, NP_004295, ACI47591, or EDL38401.1). Human and murine ALK protein sequences are publicly available. One of ordinary skill in the art can identify additional ALK protein sequences, including ALK variants.

An exemplary ALK full-length amino acid sequence from Homo Sapiens is provided below (ALK cytoplasmic portion in bold font):

TASSGGMGAIGLLWLLPLLLSTAAVGSGMGTGQRAGSPAAGPPLQPREPL

SYSRLQRKSLAVDEVVPSLFRVYARDLLLPPSSSELKAGRPEARGSLALD

CAPLLRLLGPAPGVSWTAGSPAPAEARTLSRVLKGGSVRKLRRAKQLVLE

LGEEAILEGCVGPPGEAAVGLLQFNLSELFSWWIRQGEGRLRIRLMPEKK

ASEVGREGRLSAAIRASQPRLLFQIFGTGHSSLESPTNMPSPSPDYFTWN

LTWIMKDSFPFLSHRSRYGLECSFDFPCELEYSPPLHDLRNQSWSWRRIP

SEEASQMDLLDGPGAERSKEMPRGSFLLLNTSADSKHTILSPWMRSSSEH

CTLAVSVHRHLQPSGRYIAQLLPHNEAAREILLMPTPGKHGWTVLQGRIG

RPDNPFRVALEYISSGNRSLSAVDFFALKNCSEGTSPGSKMALQSSFTCW

NGTVLQLGQACDFHQDCAQGEDESQMCRKLPVGFYCNFEDGFCGWTQGTL

SPHTPQWQVRTLKDARFQDHQDHALLLSTTDVPASESATVTSATFPAPIK

SSPCELRMSWLIRGVLRGNVSLVLVENKTGKEQGRMVWHVAAYEGLSLWQ

WMVLPLLDVSDRFWLQMVAWWGQGSRAIVAFDNISISLDCYLTISGEDKI

LQNTAPKSRNLFERNPNKELKPGENSPRQTPIFDPTVHWLFTTCGASGPH

GPTQAQCNNAYQNSNLSVEVGSEGPLKGIQIWKVPATDTYSISGYGAAGG

KGGKNTMMRSHGVSVLGIFNLEKDDMLYILVGQQGEDACPSTNQLIQKVC

IGENNVIEEEIRVNRSVHEWAGGGGGGGGATYVFKMKDGVPVPLIIAAGG

GGRAYGAKTDTFHPERLENNSSVLGLNGNSGAAGGGGGWNDNTSLLWAGK

SLQEGATGGHSCPQAMKKWGWETRGGFGGGGGGCSSGGGGGGYIGGNAAS

NNDPEMDGEDGVSFISPLGILYTPALKVMEGHGEVNIKHYLNCSHCEVDE

CHMDPESHKVICFCDHGTVLAEDGVSCIVSPTPEPHLPLSLILSVVTSAL

VAALVLAFSGIMIVYRRKHQELQAMQMELQSPEYKLSKLRTSTIMTDYNP

NYCFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSP

LQVAVKTLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFI

LLELMAGGDLKSFLRETRPRPSQPSSIAMLDLLHVARDIACGCQYLEENH

FIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRASYYRKGGCAMLPVK

WMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTS

GGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVIN

TALPIEYGPLVEEEEKVPVRPKDPEGVPPLLVSQQAKREEERSPAAPPPL

PTTSSGKAAKKPTAAEISVRVPRGPAVEGGHVNMAFSQSNPPSELHKVHG

SRNKPTSLWNPTYGSWFTEKPTKKNNPIAKKEPHDRGNLGLEGSCTVPPN

VATGRLPGASLLLEPSSLTANMKEVPLFRLRHFPCGNVNYGYQQQGLPLE

AATAPGAGHYEDTILKSKNSMNQPGP

An exemplary full-length ALK amino acid sequence from Homo Sapiens is provided below:

G A A A V V A A G T S R R L C S E G R G

A P R C F P A A L W S A T Q S R G R * *

W V R R G R Q D F G R P C P E R P Q L L

P P G P L Q C L R T L R S R G A G E S K

D A A N L R S A G A G I H A Q K F S R Q

T V R S L P A A E R * L E G A Q D G S L

R P R F P P R P G R R A W R S Q K E R K

R R P G Q R A A A G S R R S Q P * K L Q

R L E A A P R G D R P Q L R L R G A G E

D G T Q L P P P F N H S S S S V P S A A

S Y R R G R G T R R G E R E A Q G P S Q

* A Q C A * V S L D S P L S F Q V C F I

* T P A R L R A V G G K Q E T C A H A Q

S S G D Q V E G A A G Y Q G L F R A S S

H L G E S E G * G W A R R A V * T A S S

G G M G A I G L L W L L P L L L S T A A

V G S G M G T G Q R A G S P A A G P P L

Q P R E P L S Y S R L Q R K S L A V D F

V V P S L F R V Y A R D L L L P P S S S

E L K A G R P E A R G S L A L D C A P L

L R L L G P A P G V S W T A G S P A P A

E A R T L S R V L K G G S V R K L R R A

K Q L V L E L G E E A I L E G C V G P P

G E A A V G L L Q F N L S E L F S W W I

R Q G E G R L R I R L M P E K K A S E V

G R E G R L S A A I R A S Q P R L L F Q

I F G T G H S S L E S P T N M P S P S P

D Y F T W N L T W I M K D S F P F L S H

R S R Y G L E C S F D F P C E L E Y S P

P L H D L R N Q S W S W R R I P S E E A

S Q M D L L D G P G A E R S K E M P R G

S F L L L N T S A D S K H T I L S P W M

R S S S E H C T L A V S V H R H L Q P S

G R Y I A Q L L P H N E A A R E I L L M

P T P G K H G W T V L Q G R I G R P D N

P F R V A L E Y I S S G N R S L S A V D

F F A L K N C S E G T S P G S K M A L Q

S S F T C W N G T V L Q L G Q A C D F H

Q D C A Q G E D E S Q M C R K L P V G F

Y C N F E D G F C G W T Q G T L S P H T

P Q W Q V R T L K D A R F Q D H Q D H A

L L L S T T D V P A S E S A T V T S A T

F P A P I K S S P C E L R M S W L I R G

V L R G N V S L V L V E N K T G K E Q G

R M V W H V A A Y E G L S L W Q W M V L

P L L D V S D R F W L Q M V A W W G Q G

S R A I V A F D N I S I S L D C Y L T I

S G E D K I L Q N T A P K S R N L F E R

N P N K E L K P G E N S P R Q T P I F D

P T V H W L F T T C G A S G P H G P T Q

A Q C N N A Y Q N S N L S V E V G S E G

P L K G I Q I W K V P A T D T Y S I S G

Y G A A G G K G G K N T M M R S H G V S

V L G I F N L E K D D M L Y I L V G Q Q

G E D A C P S T N Q L I Q K V C I G E N

N V I E E E I R V N R S V H E W A G G G

G G G G G A T Y V F K M K D G V P V P L

I I A A G G G G R A Y G A K T D T F H P

E R L E N N S S V L G L N G N S G A A G

G G G G W N D N T S L L W A G K S L Q E

G A T G G H S C P Q A M K K W G W E T R

G G F G G G G G G C S S G G G G G G Y I

G G N A A S N N D P E M D G E D G V S F

I S P L G I L Y T P A L K V M E G H G E

V N I K H Y L N C S H C E V D E C H M D

P E S H K V I C F C D H G T V L A E D G

V S C I V S P T P E P H L P L S L I L S

V V T S A L V A A L V L A F S G I M I V

Y R R K H Q E L Q A M Q M E L Q S P E Y

K L S K L R T S T I M T D Y N P N Y C F

A G K T S S I S D L K E V P R K N I T L

I R G L G H G A F G E V Y E G Q V S G M

P N D P S P L Q V A V K T L P E V C S E

Q D E L D F L M E A L I I S K F N H Q N

I V R C I G V S L Q S L P R F I L L E L

M A G G D L K S F L R E T R P R P S Q P

S S L A M L D L L H V A R D I A C G C Q

Y L E E N H F I H R D I A A R N C L L T

C P G P G R V A K I G D F G M A R D I Y

R A S Y Y R K G G C A M L P V K W M P P

E A F M E G I F T S K T D T W S F G V L

L W E I F S L G Y M P Y P S K S N Q E V

L E F V T S G G R M D P P K N C P G P V

Y R I M T Q C W Q H Q P E D R P N F A I

I L E R I E Y C T Q D P D V I N T A L P

I E Y G P L V E E E E K V P V R P K D P

E G V P P L L V S Q Q A K R E E E R S P

A A P P P L P T T S S G K A A K K P T A

A E I S V R V P R G P A V E G G H V N M

A F S Q S N P P S E L H K V H G S R N K

P T S L W N P T Y G S W F T E K P T K K

N N P I A K K E P H D R G N L G L E G S

C T V P P N V A T G R L P G A S L L L E

P S S L T A N M K E V P L F R L R H F P

C G N V N Y G Y Q Q Q G L P L E A A T A

P G A G H Y E D T I L K S K N S M N Q P

G P * A R S H T H F S S L G S L R P W R

R E R Q W L L H K P E T K C H V L F C A

N L F * S T T K K A V F * K C F R K V L

S M G S S Y S F E R R K Y H K N E * * I

Q G P D V V A * G F Y A C L L Y T S L C

F F Q I V C A L L Q C S Q N * L L L C F

I V G V I D V S L P C * C G H E P F E G

R G N G N K G V I C N D *

An exemplary Homo Sapiens ALK amino acid sequence from GenBank™ accession no. NP_004295 is provided below:

1
MGAIGLLWLL PLLLSTAAVG SGMGTGQRAG SPAAGPPLQP REPLSYSRLQ RKSLAVDFVV

61
PSLFRVYARD LLLPPSSSEL KAGRPEARGS LALDCAPLLR LLGPAPGVSW TAGSPAPAEA

121
RTLSRVLKGG SVRKLRRAKQ LVLELGEEAI LEGCVGPPGE AAVGLLQFNL SELFSWWIRQ

181
GEGRLRIRLM PEKKASEVGR EGRLSAAIRA SQPRLLFQIF GTGHSSLESP TNMPSPSPDY

241
FTWNLTWIMK DSFPFLSHRS RYGLECSFDF PCELEYSPPL HDLRNQSWSW RRIPSEEASQ

301
MDLLDGPGAE RSKEMPRGSF LLLNTSADSK HTILSPWMRS SSEHCTLAVS VHRHLQPSGR

361
YIAQLLPHNE AAREILLMPT PGKHGWTVLQ GRIGRPDNPF RVALEYISSG NRSLSAVDFF

421
ALKNCSEGTS PGSKMALQSS FTCWNGTVLQ LGQACDFHQD CAQGEDESQM CRKLPVGFYC

481
NFEDGFCGWT QGTLSPHTPQ WQVRTLKDAR FQDHQDHALL LSTTDVPASE SATVTSATFP

541
APIKSSPCEL RMSWLIRGVL RGNVSLVLVE NKTGKEQGRM VWHVAAYEGL SLWQWMVLPL

601
LDVSDRFWLQ MVAWWGQGSR AIVAFDNISI SLDCYLTISG EDKILQNTAP KSRNLFERNP

661
NKELKPGENS PRQTPIFDPT VHWLFTTCGA SGPHGPTQAQ CNNAYQNSNL SVEVGSEGPL

721
KGIQIWKVPA TDTYSISGYG AAGGKGGKNT MMRSHGVSVL GIFNLEKDDM LYILVGQQGE

781
DACPSTNQLI QKVCIGENNV IEEEIRVNRS VHEWAGGGGG GGGATYVFKM KDGVPVPLII

841
AAGGGGRAYG AKTDTFHPER LENNSSVLGL NGNSGAAGGG GGWNDNTSLL WAGKSLQEGA

901
TGGHSCPQAM KKWGWETRGG FGGGGGGCSS GGGGGGYIGG NAASNNDPEM DGEDGVSFIS

961
PLGILYTPAL KVMEGHGEVN IKHYLNCSHC EVDECHMDPE SHKVICFCDH GTVLAEDGVS

1021
CIVSPTPEPH LPLSLILSVV TSALVAALVL AFSGIMIVYR RKHQELQAMQ MELQSPEYKL

1081
SKLRTSTIMT DYNPNYCFAG KTSSISDLKE VPRKNITLIR GLGHGAFGEV YEGQVSGMPN

1141
DPSPLQVAVK TLPEVCSEQD ELDFLMEALI ISKFNHQNIV RCIGVSLQSL PRFILLELMA

1201
GGDLKSFLRE TRPRPSQPSS LAMLDLLHVA RDIACGCQYL EENHFIHRDI AARNCLLTCP

1261
GPGRVAKIGD FGMARDIYRA SYYRKGGCAM LPVKWMPPEA FMEGIFTSKT DTWSFGVLLW

1321
EIFSLGYMPY PSKSNQEVLE FVTSGGRMDP PKNCPGPVYR IMTQCWQHQP EDRPNFAIIL

1381
ERIEYCTQDP DVINTALPIE YGPLVEEEEK VPVRPKDPEG VPPLLVSQQA KREEERSPAA

1441
PPPLPTTSSG KAAKKPTAAE ISVRVPRGPA VEGGHVNMAF SQSNPPSELH KVHGSRNKPT

1501
SLWNPTYGSW FTEKPTKKNN PIAKKEPHDR GNLGLEGSCT VPPNVATGRL PGASLLLEPS

1561
SLTANMKEVP LFRLRHFPCG NVNYGYQQQG LPLEAATAPG AGHYEDTILK SKNSMNQPGP

An exemplary Homo Sapiens ALK polypeptide sequence from UniProt Accession No. Q9UM73 is provided below (extracellular domain (amino acids 19-1038) provided in bold font):

MGAIGLLWLLPLLLSTAAVGSGMGTGQRAGSPAAGPPLQPREPLSYSRLQ

RKSLAVDFVVPSLFRVYARDLLLPPSSSELKAGRPEARGSLALDCAPLLR

LLGPAPGVSWTAGSPAPAEARTLSRVLKGGSVRKLRRAKQLVLELGEEAI

LEGCVGPPGEAAVGLLQFNLSELFSWWIRQGEGRLRIRLMPEKKASEVGR

EGRLSAAIRASQPRLLFQIFGTGHSSLESPTNMPSPSPDYFTWNLTWIMK

DSFPFLSHRSRYGLECSFDFPCELEYSPPLHDLRNQSWSWRRIPSEEASQ

MDLLDGPGAERSKEMPRGSFLLLNTSADSKHTILSPWMRSSSEHCTLAVS

VHRHLQPSGRYIAQLLPHNEAAREILLMPTPGKHGWTVLQGRIGRPDNPF

RVALEYISSGNRSLSAVDFFALKNCSEGTSPGSKMALQSSFTCWNGTVLQ

LGQACDFHQDCAQGEDESQMCRKLPVGFYCNFEDGFCGWTQGTLSPHTPQ

WQVRTLKDARFQDHQDHALLLSTTDVPASESATVTSATFPAPIKSSPCEL

RMSWLIRGVLRGNVSLVLVENKTGKEQGRMVWHVAAYEGLSLWQWMVLPL

LDVSDRFWLQMVAWWGQGSRAIVAFDNISISLDCYLTISGEDKILQNTAP

KSRNLFERNPNKELKPGENSPRQTPIFDPTVHWLFTTCGASGPHGPTQAQ

CNNAYQNSNLSVEVGSEGPLKGIQIWKVPATDTYSISGYGAAGGKGGKNT

MMRSHGVSVLGIFNLEKDDMLYILVGQQGEDACPSTNQLIQKVCIGENNV

IEEEIRVNRSVHEWAGGGGGGGGATYVFKMKDGVPVPLIIAAGGGGRAYG

AKTDTFHPERLENNSSVLGLNGNSGAAGGGGGWNDNTSLLWAGKSLQEGA

TGGHSCPQAMKKWGWETRGGFGGGGGGCSSGGGGGGYIGGNAASNNDPEM

DGEDGVSFISPLGILYTPALKVMEGHGEVNIKHYLNCSHCEVDECHMDPE

SHKVICFCDHGTVLAEDGVSCIVSPTPEPHLPLSLILSVVTSALVAALVL

AFSGIMIVYRRKHQELQAMQMELQSPEYKLSKLRTSTIMTDYNPNYCFAG

KTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVK

TLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLELMA

GGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDI

AARNCLLTCPGPGRVAKIGDFGMARDIYRASYYRKGGCAMLPVKWMPPEA

FMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDP

PKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIE

YGPLVEEEEKVPVRPKDPEGVPPLLVSQQAKREEERSPAAPPPLPTTSSG

KAAKKPTAAEISVRVPRGPAVEGGHVNMAFSQSNPPSELHKVHGSRNKPT

SLWNPTYGSWFTEKPTKKNNPIAKKEPHDRGNLGLEGSCTVPPNVATGRL

PGASLLLEPSSLTANMKEVPLFRLRHFPCGNVNYGYQQQGLPLEAATAPG

AGHYEDTILKSKNSMNQPGP

An exemplary ALK full-length amino acid sequence from Mus musculus is provided below:

1
MGQRQSILKR CPEGSFLLLN TSADSKHTIL SPWMRSSSDH CTLAVSVHRH LQPSGRYVAQ

61
LLPHNEAGRE ILLVPTPGKH GWTVLQGRVG RPANPFRVAL EYISSGNRSL SAVDFFALKN

121
CSEGTSPGSK MALQSSFTCW NGTVLQLGQA CDFHQDCAQG EDEGQLCSKL PAGFYCNFEN

181
GFCGWTQSPL SPHMPRWQVR TLRDAHSQGH QGRALLLSTT DILASEGATV TSATFPAPMK

241
NSPCELRMSW LIRGVLRGNV SLVLVENKTG KEQSRTVWHV ATDEGLSLWQ HTVLSLLDVT

301
DRFWLQIVTW WGPGSRATVG FDNISISLDC YLTISGEEKM SLNSVPKSRN LFEKNPNKES

361
KSWANISGPT PIFDPTVHWL FTTCGASGPH GPTQAQCNNA YQNSNLSVVV GSEGPLKGVQ

421
IWKVPATDTY SISGYGAAGG KGGKNTMMRS HGVSVLGIFN LEKGDTLYIL VGQQGEDACP

481
RANQLIQKVC VGENNVIEEE IRVNRSVHEW AGGGGGGGGA TYVFKMKDGV PVPLIIAAGG

541
GGRAYGAKTE TFHPERLESN SSVLGLNGNS GAAGGGGGWN DNTSLLWAGK SLLEGAAGGH

601
SCPQAMKKWG WETRGGFGGG GGGGAPQVEE AEDI

By “ALK polynucleotide” is meant any nucleic acid molecule encoding an ALK polypeptide or fragment thereof (e.g., antigen or antigen protein). In some embodiments, the ALK polynucleotide is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to a polynucleotide encoding full-length ALK protein. In some embodiments, the ALK polynucleotide is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to a polynucleotide encoding full-length ALK protein in Homo Sapiens. In some embodiments, the ALK polynucleotide is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to a polynucleotide encoding a full-length murine ALK protein. In some embodiments, the ALK polynucleotide encodes an ALK extracellular domain. In some embodiments, the ALK polynucleotide is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to a polypeptide encoding an ALK extracellular domain in Homo Sapiens. In some embodiments, the ALK polynucleotide is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to a polypeptide encoding a murine ALK extracellular domain. In some embodiments, the ALK polynucleotide encodes an ALK intracellular domain. In some embodiments, the ALK polynucleotide is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to a polynucleotide encoding an ALK intracellular domain in Homo Sapiens. In some embodiments, the ALK polynucleotide is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to a polynucleotide encoding a murine ALK intracellular domain. In some embodiments, the ALK polynucleotide is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to a polynucleotide encoding an ALK amino acid sequence associated with GenBank™ Accession Nos.: BAD92714.1, ACY79563, NP_004295, EDL38401.1 or ACI47591. Human and murine ALK polynucleotide sequences are publicly available. One of ordinary skill in the art can identify additional ALK polynucleotide sequences, including ALK variants.

An exemplary Homo Sapiens ALK amino acid sequence from GenBank™ accession no. NM_004304 is provided below:

1
agatgcgatc cagcggctct gggggcggca gcggtggtag cagctggtac ctcccgccgc

61
ctctgttcgg agggtcgcgg ggcaccgagg tgctttccgg ccgccctctg gtcggccacc

121
caaagccgcg ggcgctgatg atgggtgagg agggggcggc aagatttcgg gcgcccctgc

181
cctgaacgcc ctcagctgct gccgccgggg ccgctccagt gcctgcgaac tctgaggagc

241
cgaggcgccg gtgagagcaa ggacgctgca aacttgcgca gcgcgggggc tgggattcac

301
gcccagaagt tcagcaggca gacagtccga agccttcccg cagcggagag atagcttgag

361
ggtgcgcaag acggcagcct ccgccctcgg ttcccgccca gaccgggcag aagagcttgg

421
aggagccaaa aggaacgcaa aaggcggcca ggacagcgtg cagcagctgg gagccgccgt

481
tctcagcctt aaaagttgca gagattggag gctgccccga gaggggacag accccagctc

541
cgactgcggg gggcaggaga ggacggtacc caactgccac ctcccttcaa ccatagtagt

601
tcctctgtac cgagcgcagc gagctacaga cgggggcgcg gcactcggcg cggagagcgg

661
gaggctcaag gtcccagcca gtgagcccag tgtgcttgag tgtctctgga ctcgcccctg

721
agcttccagg tctgtttcat ttagactcct gctcgcctcc gtgcagttgg gggaaagcaa

781
gagacttgcg cgcacgcaca gtcctctgga gatcaggtgg aaggagccgc tgggtaccaa

841
ggactgttca gagcctcttc ccatctcggg gagagcgaag ggtgaggctg ggcccggaga

901
gcagtgtaaa cggcctcctc cggcgggatg ggagccatcg ggctcctgtg gctcctgccg

961
ctgctgcttt ccacggcagc tgtgggctcc gggatgggga ccggccagcg cgcgggctcc

1021
ccagctgcgg ggccgccgct gcagccccgg gagccactca gctactcgcg cctgcagagg

1081
aagagtctgg cagttgactt cgtggtgccc tcgctcttcc gtgtctacgc ccgggaccta

1141
ctgctgccac catcctcctc ggagctgaag gctggcaggc ccgaggcccg cggctcgcta

1201
gctctggact gcgccccgct gctcaggttg ctggggccgg cgccgggggt ctcctggacc

1261
gccggttcac cagccccggc agaggcccgg acgctgtcca gggtgctgaa gggcggctcc

1321
gtgcgcaagc tccggcgtgc caagcagttg gtgctggagc tgggcgagga ggcgatcttg

1381
gagggttgcg tcgggccccc cggggaggcg gctgtggggc tgctccagtt caatctcagc

1441
gagctgttca gttggtggat tcgccaaggc gaagggcgac tgaggatccg cctgatgccc

1501
gagaagaagg cgtcggaagt gggcagagag ggaaggctgt ccgcggcaat tcgcgcctcc

1561
cagccccgcc ttctcttcca gatcttcggg actggtcata gctccttgga atcaccaaca

1621
aacatgcctt ctccttctcc tgattatttt acatggaatc tcacctggat aatgaaagac

1681
tccttccctt tcctgtctca tcgcagccga tatggtctgg agtgcagctt tgacttcccc

1741
tgtgagctgg agtattcccc tccactgcat gacctcagga accagagctg gtcctggcgc

1801
cgcatcccct ccgaggaggc ctcccagatg gacttgctgg atgggcctgg ggcagagcgt

1861
tctaaggaga tgcccagagg ctcctttctc cttctcaaca cctcagctga ctccaagcac

1921
accatcctga gtccgtggat gaggagcagc agtgagcact gcacactggc cgtctcggtg

1981
cacaggcacc tgcagccctc tggaaggtac attgcccagc tgctgcccca caacgaggct

2041
gcaagagaga tcctcctgat gcccactcca gggaagcatg gttggacagt gctccaggga

2101
agaatcgggc gtccagacaa cccatttcga gtggccctgg aatacatctc cagtggaaac

2161
cgcagcttgt ctgcagtgga cttctttgcc ctgaagaact gcagtgaagg aacatcccca

2221
ggctccaaga tggccctgca gagctccttc acttgttgga atgggacagt cctccagctt

2281
gggcaggcct gtgacttcca ccaggactgt gcccagggag aagatgagag ccagatgtgc

2341
cggaaactgc ctgtgggttt ttactgcaac tttgaagatg gcttctgtgg ctggacccaa

2401
ggcacactgt caccccacac tcctcaatgg caggtcagga ccctaaagga tgcccggttc

2461
caggaccacc aagaccatgc tctattgctc agtaccactg atgtccccgc ttctgaaagt

2521
gctacagtga ccagtgctac gtttcctgca ccgatcaaga gctctccatg tgagctccga

2581
atgtcctggc tcattcgtgg agtcttgagg ggaaacgtgt ccttggtgct agtggagaac

2641
aaaaccggga aggagcaagg caggatggtc tggcatgtcg ccgcctatga aggcttgagc

2701
ctgtggcagt ggatggtgtt gcctctcctc gatgtgtctg acaggttctg gctgcagatg

2761
gtcgcatggt ggggacaagg atccagagcc atcgtggctt ttgacaatat ctccatcagc

2821
ctggactgct acctcaccat tagcggagag gacaagatcc tgcagaatac agcacccaaa

2881
tcaagaaacc tgtttgagag aaacccaaac aaggagctga aacccgggga aaattcacca

2941
agacagaccc ccatctttga ccctacagtt cattggctgt tcaccacatg tggggccagc

3001
gggccccatg gccccaccca ggcacagtgc aacaacgcct accagaactc caacctgagc

3061
gtggaggtgg ggagcgaggg ccccctgaaa ggcatccaga tctggaaggt gccagccacc

3121
gacacctaca gcatctcggg ctacggagct gctggcggga aaggcgggaa gaacaccatg

3181
atgcggtccc acggcgtgtc tgtgctgggc atcttcaacc tggagaagga tgacatgctg

3241
tacatcctgg ttgggcagca gggagaggac gcctgcccca gtacaaacca gttaatccag

3301
aaagtctgca ttggagagaa caatgtgata gaagaagaaa tccgtgtgaa cagaagcgtg

3361
catgagtggg caggaggcgg aggaggaggg ggtggagcca cctacgtatt taagatgaag

3421
gatggagtgc cggtgcccct gatcattgca gccggaggtg gtggcagggc ctacggggcc

3481
aagacagaca cgttccaccc agagagactg gagaataact cctcggttct agggctaaac

3541
ggcaattccg gagccgcagg tggtggaggt ggctggaatg ataacacttc cttgctctgg

3601
gccggaaaat ctttgcagga gggtgccacc ggaggacatt cctgccccca ggccatgaag

3661
aagtgggggt gggagacaag agggggtttc ggagggggtg gaggggggtg ctcctcaggt

3721
ggaggaggcg gaggatatat aggcggcaat gcagcctcaa acaatgaccc cgaaatggat

3781
ggggaagatg gggtttcctt catcagtcca ctgggcatcc tgtacacccc agctttaaaa

3841
gtgatggaag gccacgggga agtgaatatt aagcattatc taaactgcag tcactgtgag

3901
gtagacgaat gtcacatgga ccctgaaagc cacaaggtca tctgcttctg tgaccacggg

3961
acggtgctgg ctgaggatgg cgtctcctgc attgtgtcac ccaccccgga gccacacctg

4021
ccactctcgc tgatcctctc tgtggtgacc tctgccctcg tggccgccct ggtcctggct

4081
ttctccggca tcatgattgt gtaccgccgg aagcaccagg agctgcaagc catgcagatg

4141
gagctgcaga gccctgagta caagctgagc aagctccgca cctcgaccat catgaccgac

4201
tacaacccca actactgctt tgctggcaag acctcctcca tcagtgacct gaaggaggtg

4261
ccgcggaaaa acatcaccct cattcggggt ctgggccatg gcgcctttgg ggaggtgtat

4321
gaaggccagg tgtccggaat gcccaacgac ccaagccccc tgcaagtggc tgtgaagacg

4381
ctgcctgaag tgtgctctga acaggacgaa ctggatttcc tcatggaagc cctgatcatc

4441
agcaaattca accaccagaa cattgttcgc tgcattgggg tgagcctgca atccctgccc

4501
cggttcatcc tgctggagct catggcgggg ggagacctca agtccttcct ccgagagacc

4561
cgccctcgcc cgagccagcc ctcctccctg gccatgctgg accttctgca cgtggctcgg

4621
gacattgcct gtggctgtca gtatttggag gaaaaccact tcatccaccg agacattgct

4681
gccagaaact gcctcttgac ctgtccaggc cctggaagag tggccaagat tggagacttc

4741
gggatggccc gagacatcta cagggcgagc tactatagaa agggaggctg tgccatgctg

4801
ccagttaagt ggatgccccc agaggccttc atggaaggaa tattcacttc taaaacagac

4861
acatggtcct ttggagtgct gctatgggaa atcttttctc ttggatatat gccatacccc

4921
agcaaaagca accaggaagt tctggagttt gtcaccagtg gaggccggat ggacccaccc

4981
aagaactgcc ctgggcctgt ataccggata atgactcagt gctggcaaca tcagcctgaa

5041
gacaggccca actttgccat cattttggag aggattgaat actgcaccca ggacccggat

5101
gtaatcaaca ccgctttgcc gatagaatat ggtccacttg tggaagagga agagaaagtg

5161
cctgtgaggc ccaaggaccc tgagggggtt cctcctctcc tggtctctca acaggcaaaa

5221
cgggaggagg agcgcagccc agctgcccca ccacctctgc ctaccacctc ctctggcaag

5281
gctgcaaaga aacccacagc tgcagagatc tctgttcgag tccctagagg gccggccgtg

5341
gaagggggac acgtgaatat ggcattctct cagtccaacc ctccttcgga gttgcacaag

5401
gtccacggat ccagaaacaa gcccaccagc ttgtggaacc caacgtacgg ctcctggttt

5461
acagagaaac ccaccaaaaa gaataatcct atagcaaaga aggagccaca cgacaggggt

5521
aacctggggc tggagggaag ctgtactgtc ccacctaacg ttgcaactgg gagacttccg

5581
ggggcctcac tgctcctaga gccctcttcg ctgactgcca atatgaagga ggtacctctg

5641
ttcaggctac gtcacttccc ttgtgggaat gtcaattacg gctaccagca acagggcttg

5701
cccttagaag ccgctactgc ccctggagct ggtcattacg aggataccat tctgaaaagc

5761
aagaatagca tgaaccagcc tgggccctga gctcggtcgc acactcactt ctcttccttg

5821
ggatccctaa gaccgtggag gagagagagg caatggctcc ttcacaaacc agagaccaaa

5881
tgtcacgttt tgttttgtgc caacctattt tgaagtacca ccaaaaaagc tgtattttga

5941
aaatgcttta gaaaggtttt gagcatgggt tcatcctatt ctttcgaaag aagaaaatat

6001
cataaaaatg agtgataaat acaaggccca gatgtggttg cataaggttt ttatgcatgt

6061
ttgttgtata cttccttatg cttctttcaa attgtgtgtg ctctgcttca atgtagtcag

6121
aattagctgc ttctatgttt catagttggg gtcatagatg tttccttgcc ttgttgatgt

6181
ggacatgagc catttgaggg gagagggaac ggaaataaag gagttatttg taatgactaa

An exemplary full-length ALK nucleic acid sequence from Homo Sapiens is provided below:

2
ggggcggcagcggtggtagcagctggtacctcccgccgcctctgttcggagggtcgcggg
61

62
gcaccgaggtgctttccggccgccctctggtcggccacccaaagccgcgggcgctgatga
121

122
tgggtgaggagggggcggcaagatttcgggcgcccctgccctgaacgccctcagctgctg
181

182
ccgccggggccgctccagtgcctgcgaactctgaggagccgaggcgccggtgagagcaag
241

242
gacgctgcaaacttgcgcagcgcgggggctgggattcacgcccagaagttcagcaggcag
301

302
acagtccgaagccttcccgcagcggagagatagcttgagggtgcgcaagacggcagcctc
361

362
cgccctcggttcccgcccagaccgggcagaagagcttggaggagccaaaaggaacgcaaa
421

422
aggcggccaggacagcgtgcagcagctgggagccgccgttctcagccttaaaagttgcag
481

482
agattggaggctgccccgagaggggacagaccccagctccgactgcggggggcaggagag
541

542
gacggtacccaactgccacctcccttcaaccatagtagttcctctgtaccgagcgcagcg
601

602
agctacagacgggggcgcggcactcggcgcggagagcgggaggctcaaggtcccagccag
661

662
tgagcccagtgtgcttgagtgtctctggactcgcccctgagcttccaggtctgtttcatt
721

722
tagactcctgctcgcctccgtgcagttgggggaaagcaagagacttgcgcgcacgcacag
781

782
tcctctggagatcaggtggaaggagccgctgggtaccaaggactgttcagagcctcttcc
841

842
catctcggggagagcgaagggtgaggctgggcccggagagcagtgtaaacggcctcctcc
901

902
ggcgggatgggagccatcgggctcctgtggctcctgccgctgctgctttccacggcagct
961

962
gtgggctccgggatggggaccggccagcgcgcgggctccccagctgcggggccgccgctg
1021

1022
cagccccgggagccactcagctactcgcgcctgcagaggaagagtctggcagttgacttc
1081

1082
gtggtgccctcgctcttccgtgtctacgcccgggacctactgctgccaccatcctcctcg
1141

1142
gagctgaaggctggcaggcccgaggcccgcggctcgctagctctggactgcgccccgctg
1201

1202
ctcaggttgctggggccggcgccgggggtctcctggaccgccggttcaccagccccggca
1261

1262
gaggcccggacgctgtccagggtgctgaagggcggctccgtgcgcaagctccggcgtgcc
1321

1322
aagcagttggtgctggagctgggcgaggaggcgatcttggagggttgcgtcgggcccccc
1381

1382
ggggaggcggctgtggggctgctccagttcaatctcagcgagctgttcagttggtggatt
1441

1442
cgccaaggcgaagggcgactgaggatccgcctgatgcccgagaagaaggcgtcggaagtg
1501

1502
ggcagagagggaaggctgtccgcggcaattcgcgcctcccagccccgccttctcttccag
1561

1562
atcttcgggactggtcatagctccttggaatcaccaacaaacatgccttctccttctcct
1621

1622
gattattttacatggaatctcacctggataatgaaagactccttccctttcctgtctcat
1681

1682
cgcagccgatatggtctggagtgcagctttgacttcccctgtgagctggagtattcccct
1741

1742
ccactgcatgacctcaggaaccagagctggtcctggcgccgcatcccctccgaggaggcc
1801

1802
tcccagatggacttgctggatgggcctggggcagagcgttctaaggagatgcccagaggc
1861

1862
tcctttctccttctcaacacctcagctgactccaagcacaccatcctgagtccgtggatg
1921

1922
aggagcagcagtgagcactgcacactggccgtctcggtgcacaggcacctgcagccctct
1981

1982
ggaaggtacattgcccagctgctgccccacaacgaggctgcaagagagatcctcctgatg
2041

2042
cccactccagggaagcatggttggacagtgctccagggaagaatcgggcgtccagacaac
2101

2102
ccatttcgagtggccctggaatacatctccagtggaaaccgcagcttgtctgcagtggac
2161

2162
ttctttgccctgaagaactgcagtgaaggaacatccccaggctccaagatggccctgcag
2221

2222
agctccttcacttgttggaatgggacagtcctccagcttgggcaggcctgtgacttccac
2281

2282
caggactgtgcccagggagaagatgagagccagatgtgccggaaactgcctgtgggtttt
2341

2342
tactgcaactttgaagatggcttctgtggctggacccaaggcacactgtcaccccacact
2401

2402
cctcaatggcaggtcaggaccctaaaggatgcccggttccaggaccaccaagaccatgct
2461

2462
ctattgctcagtaccactgatgtccccgcttctgaaagtgctacagtgaccagtgctacg
2521

2522
tttcctgcaccgatcaagagctctccatgtgagctccgaatgtcctggctcattcgtgga
2581

2582
gtcttgaggggaaacgtgtccttggtgctagtggagaacaaaaccgggaaggagcaaggc
2641

2642
aggatggtctggcatgtcgccgcctatgaaggcttgagcctgtggcagtggatggtgttg
2701

2702
cctctcctcgatgtgtctgacaggttctggctgcagatggtcgcatggtggggacaagga
2761

2762
tccagagccatcgtggcttttgacaatatctccatcagcctggactgctacctcaccatt
2821

2822
agcggagaggacaagatcctgcagaatacagcacccaaatcaagaaacctgtttgagaga
2881

2882
aacccaaacaaggagctgaaacccggggaaaattcaccaagacagacccccatctttgac
2941

2942
cctacagttcattggctgttcaccacatgtggggccagcgggccccatggccccacccag
3001

3002
gcacagtgcaacaacgcctaccagaactccaacctgagcgtggaggtggggagcgagggc
3061

3062
cccctgaaaggcatccagatctggaaggtgccagccaccgacacctacagcatctcgggc
3121

3122
tacggagctgctggcgggaaaggcgggaagaacaccatgatgcggtcccacggcgtgtct
3181

3182
gtgctgggcatcttcaacctggagaaggatgacatgctgtacatcctggttgggcagcag
3241

3242
ggagaggacgcctgccccagtacaaaccagttaatccagaaagtctgcattggagagaac
3301

3302
aatgtgatagaagaagaaatccgtgtgaacagaagcgtgcatgagtgggcaggaggcgga
3361

3362
ggaggagggggtggagccacctacgtatttaagatgaaggatggagtgccggtgcccctg
3421

3422
atcattgcagccggaggtggtggcagggcctacggggccaagacagacacgttccaccca
3481

3482
gagagactggagaataactcctcggttctagggctaaacggcaattccggagccgcaggt
3541

3542
ggtggaggtggctggaatgataacacttccttgctctgggccggaaaatctttgcaggag
3601

3602
ggtgccaccggaggacattcctgcccccaggccatgaagaagtgggggtgggagacaaga
3661

3662
gggggtttcggagggggtggaggggggtgctcctcaggtggaggaggcggaggatatata
3721

3722
ggcggcaatgcagcctcaaacaatgaccccgaaatggatggggaagatggggtttccttc
3781

3782
atcagtccactgggcatcctgtacaccccagctttaaaagtgatggaaggccacggggaa
3841

3842
gtgaatattaagcattatctaaactgcagtcactgtgaggtagacgaatgtcacatggac
3901

3902
cctgaaagccacaaggtcatctgcttctgtgaccacgggacggtgctggctgaggatggc
3961

3962
gtctcctgcattgtgtcacccaccccggagccacacctgccactctcgctgatcctctct
4021

4022
gtggtgacctctgccctcgtggccgccctggtcctggctttctccggcatcatgattgtg
4081

4082
taccgccggaagcaccaggagctgcaagccatgcagatggagctgcagagccctgagtac
4141

4142
aagctgagcaagctccgcacctcgaccatcatgaccgactacaaccccaactactgcttt
4201

4202
gctggcaagacctcctccatcagtgacctgaaggaggtgccgcggaaaaacatcaccctc
4261

4262
attcggggtctgggccatggcgcctttggggaggtgtatgaaggccaggtgtccggaatg
4321

4322
cccaacgacccaagccccctgcaagtggctgtgaagacgctgcctgaagtgtgctctgaa
4381

4382
caggacgaactggatttcctcatggaagccctgatcatcagcaaattcaaccaccagaac
4441

4442
attgttcgctgcattggggtgagcctgcaatccctgccccggttcatcctgctggagctc
4501

4502
atggcggggggagacctcaagtccttcctccgagagacccgccctcgcccgagccagccc
4561

4562
tcctccctggccatgctggaccttctgcacgtggctcgggacattgcctgtggctgtcag
4621

4622
tatttggaggaaaaccacttcatccaccgagacattgctgccagaaactgcctcttgacc
4681

4682
tgtccaggccctggaagagtggccaagattggagacttcgggatggcccgagacatctac
4741

4742
agggcgagctactatagaaagggaggctgtgccatgctgccagttaagtggatgccccca
4801

4802
gaggccttcatggaaggaatattcacttctaaaacagacacatggtcctttggagtgctg
4861

4862
ctatgggaaatcttttctcttggatatatgccataccccagcaaaagcaaccaggaagtt
4921

4922
ctggagtttgtcaccagtggaggccggatggacccacccaagaactgccctgggcctgta
4981

4982
taccggataatgactcagtgctggcaacatcagcctgaagacaggcccaactttgccatc
5041

5042
attttggagaggattgaatactgcacccaggacccggatgtaatcaacaccgctttgccg
5101

5102
atagaatatggtccacttgtggaagaggaagagaaagtgcctgtgaggcccaaggaccct
5161

5162
gagggggttcctcctctcctggtctctcaacaggcaaaacgggaggaggagcgcagccca
5221

5222
gctgccccaccacctctgcctaccacctcctctggcaaggctgcaaagaaacccacagct
5281

5282
gcagagatctctgttcgagtccctagagggccggccgtggaagggggacacgtgaatatg
5341

5342
gcattctctcagtccaaccctccttcggagttgcacaaggtccacggatccagaaacaag
5401

5402
cccaccagcttgtggaacccaacgtacggctcctggtttacagagaaacccaccaaaaag
5461

5462
aataatcctatagcaaagaaggagccacacgacaggggtaacctggggctggagggaagc
5521

5522
tgtactgtcccacctaacgttgcaactgggagacttccgggggcctcactgctcctagag
5581

5582
ccctcttcgctgactgccaatatgaaggaggtacctctgttcaggctacgtcacttccct
5641

5642
tgtgggaatgtcaattacggctaccagcaacagggcttgcccttagaagccgctactgcc
5701

5702
cctggagctggtcattacgaggataccattctgaaaagcaagaatagcatgaaccagcct
5761

5762
gggccctgagctcggtcgcacactcacttctcttccttgggatccctaagaccgtggagg
5821

5822
agagagaggcaatggctccttcacaaaccagagaccaaatgtcacgttttgttttgtgcc
5881

5882
aacctattttgaagtaccaccaaaaaagctgtattttgaaaatgctttagaaaggttttg
5941

5942
agcatgggttcatcctattctttcgaaagaagaaaatatcataaaaatgagtgataaata
6001

6002
caaggcccagatgtggttgcataaggtttttatgcatgtttgttgtatacttccttatgc
6061

6062
ttctttcaaattgtgtgtgctctgcttcaatgtagtcagaattagctgcttctatgtttc
6121

6122
atagttggggtcatagatgtttccttgccttgttgatgtggacatgagccatttgagggg
6181

6182
agagggaacggaaataaaggagttatttgtaatgactaaaa
6222

An exemplary Mus musculus ALK nucleic acid sequence from GenBank™ accession no. NM_007439.2 is provided below:

1
gtgttcacgc ccagaagttc agcgggcagg gtgatcgatc cgaagacttc ctgcagcgga

61
ggtcacttga gggggcgcta gaaagcagcc ccctccggtg gtccttgcct agacctggga

121
aggagcgcag aggaggtgac aggagcggag gacgtgggca agacagtgac cgactcggag

181
ccacggttca cagcctggaa agttgcagaa gattggaagc taagaggaga gctctggtcg

241
ccgagggctc cttgaacggt acctaattgc cacctccctg gtccctgagc aaaggcctct

301
acaaatgggg cgcagcacgg cgagaggcgc aggatccagc tgttgagccc agggtgtctc

361
actgtctccg aactaccccc tgactttgtc ttccgttttg ctgagaaccc ttctcgcctc

421
cttgtagctt gggaaaagca agggcgctct atagtgtaca cacagtccct gagatctagt

481
ggaaggagcc attcaggacc aaggactatt tggagccctt tcctgtttgg gggagagtga

541
agggcgaggc tggaccagca agggaaggga gactagtgta aactcgccct ccagcgggat

601
gggagctgct gggttcctgt ggctgctgcc tccactgctt ttggcagcag cctcgtactc

661
cggagctgca accgatcagc gcgcgggttc cccagcctca gggcctcctc tgcagccccg

721
ggagccgctc agttattcgc gcctgcagag gaagagtctg gcagtggact tcgttgtacc

781
ctcgctcttc cgcgtctatg cccgagacct gctgctaccg cagccacggt ccccctcgga

841
gcccgaggct ggcgggctgg aggcgcgggg atcactggcc ctggattgtg agcctctgct

901
caggctgctg gggccactgc ctggaatctc ctgggcagat ggagccagtt ctcctagtcc

961
cgaggcgggt ccgacgctgt ccagggtgct gaagggaggc tcggtgcgca agctcaggcg

1021
tgccaaacag ctggtgctgg agctgggcga ggagacgatt cttgaaggct gtattggtcc

1081
cccagaggag gtagcggctg tggggatact ccagttcaac ctcagcgagc tgttcagctg

1141
gtggattctc cacggcgaag ggaggctgag gatccgcctg atgcctgaga agaaggcatc

1201
ggaagtgggc agggagggaa ggctatccag tgcgatccga gcctcccagc cccgccttct

1261
cttccagatc ttcgggacgg gacacagctc catggagtca ccctcagaaa cgccttctcc

1321
tcctggtacc ttcatgtgga atctgacctg gacgatgaaa gactccttcc ctttcctttc

1381
ccaccgcagt cgatatggtc tggagtgcag ctttgacttc ccctgtgagc tggaatattc

1441
tcctcccctg cacaaccacg ggaatcagag ctggtcctgg cgccatgtgc cctccgagga

1501
ggcctcgagg atgaacttgc tggatgggcc agaggcagag cattctcaag agatgcccag

1561
aggctccttc ctcctcctga acacctctgc agattccaag cataccattc tgagcccatg

1621
gatgaggagc agtagtgatc actgcacact ggctgtctcc gtgcacagac atctacagcc

1681
ttcggggaga tatgttgccc agctcctacc ccacaacgaa gctggaagag agattctttt

1741
ggtgcccacc ccagggaagc atggctggac agtgctgcag gggagagtcg ggcgcccagc

1801
aaacccattt cgagtggctc tggaatacat ctccagtggc aaccggagct tgtcggcggt

1861
ggatttcttt gccctgaaga actgcagtga agggacatcc ccaggctcca agatggcatt

1921
gcagagttcc ttcacttgtt ggaatgggac cgtcctccag ctcgggcaag cctgtgattt

1981
ccaccaggac tgtgcccaag gagaagatga gggccagctg tgcagtaaac ttcctgctgg

2041
attttactgt aactttgaaa atggcttctg tggctggacc caaagtccac tctcacccca

2101
tatgccccgg tggcaagtga ggaccctaag agatgcccat tcccagggcc accaaggccg

2161
tgccctgttg ctcagcacca ctgacatcct cgcttctgaa ggtgcaacag tgaccagtgc

2221
caccttccct gcaccaatga aaaattctcc ttgtgagctc cgcatgtcct ggctcatccg

2281
cggggttttg agaggaaacg tatctctggt gctggtggag aacaaaaccg gaaaggagca

2341
aagccggact gtctggcatg tcgccactga cgaaggctta agcctgtggc agcatacagt

2401
gctgtccctc ctcgatgtga ctgacaggtt ctggctgcag atagtcacat ggtggggtcc

2461
aggatccagg gcaaccgtgg gatttgacaa catttccatc agcctcgact gctaccttac

2521
catcagtgga gaggagaaaa tgtccctgaa ttcagtaccc aaatctagaa atctgtttga

2581
gaaaaaccca aacaaggagt caaaatcctg ggcaaacata tcaggaccaa ctcccatctt

2641
cgaccctaca gttcactggc tgttcaccac gtgtggggcc agtggacctc atggccccac

2701
ccaggcacag tgcaacaacg cctaccagaa ttccaacttg agcgtggtgg tgggaagtga

2761
agggcccttg aagggagtcc agatttggaa agtgccagct actgacacct acagtatctc

2821
gggctacgga gcagctggcg ggaaaggtgg gaaaaacacc atgatgcggt cccatggcgt

2881
gtctgtcctg ggcatcttca atctggagaa aggtgacaca ctctacatcc ttgtcggtca

2941
gcaaggggag gatgcctgtc ccagggcaaa ccaactaatc cagaaagtct gtgtgggtga

3001
gaacaatgtc atagaagaag agatccgagt gaacagaagc gtgcacgagt gggcaggagg

3061
aggaggaggt gggggtggag ccacctacgt gtttaagatg aaagatggcg tgcctgtacc

3121
cctgatcatt gcagctggtg gtggtggcag ggcctatggg gccaagacag aaacgttcca

3181
cccagagaga ctggagagta actcctcggt tctagggctg aacggcaatt ccggagccgc

3241
aggtggtgga ggcggctgga atgataacac ttccttgctc tgggccggaa agtctttgct

3301
ggagggtgcc gccggaggac attcctgccc ccaggccatg aagaagtggg ggtgggagac

3361
aagagggggt ttcggagggg gtggaggggg gtgctcctca ggtggaggag gcggaggata

3421
tataggtggc aacgcagcat caaacaatga ccccgaaatg gatggggaag atggggtttc

3481
cttcatcagt ccattgggta tcctgtacac cccggcctta aaagtgatgg agggccacgg

3541
ggaagtgaat atcaagcatt atctaaactg cagtcactgc gaggtagacg aatgtcacat

3601
ggaccccgag agccacaaag tcatctgctt ctgtgatcat gggaccgtgc tggctgatga

3661
tggtgtctcc tgcattgtgt cacccacccc ggagccccac ctgccgctct cattgatcct

3721
ctccgtcgtg acctctgccc tggtggctgc ccttgttctg gcattctccg gcatcatgat

3781
tgtgtaccgt cggaagcacc aggagttgca ggctatgcag atggaactgc agagccccga

3841
gtataagctg agcaagctac ggacctcgac catcatgacc gactacaacc ccaactactg

3901
cttcgctggc aagacttcct ccatcagtga cctgaaagaa gtgccacgga aaaacatcac

3961
actcatccgg ggcctaggcc atggcgcatt tggggaggtg tatgaaggcc aggtgtctgg

4021
aatgcccaat gacccaagcc ctctacaagt ggctgtaaag acgctgccag aagtgtgttc

4081
agaacaagat gagctggact ttctcatgga agctctgatc atcagcaaat tcaaccacca

4141
gaatattgtt cgctgcatcg gggtgagtct acaagccctg ccccgcttca tcctgctgga

4201
actcatggct ggcggagacc tcaagtcctt cctcagggag acacgccctc gcccgaacca

4261
acccacctcc ctggccatgc tggaccttct gcatgtggct cgggacattg cctgtggctg

4321
tcagtaccta gaggagaatc actttatcca ccgggatatt gctgctagaa actgtctgtt

4381
gacctgccca ggagctggaa gaatagcaaa gattggagac tttgggatgg cccgagatat

4441
ctacagggcc agctactacc gaaagggagg ctgcgccatg ctgccggtca agtggatgcc

4501
ccctgaagcc ttcatggaag ggatatttac ctctaaaaca gacacatggt cttttggagt

4561
gttgctatgg gaaatatttt ctcttggata tatgccgtac cccagcaaga gcaaccagga

4621
agttctggag tttgtcacca gcggaggacg gatggacccg cctaagaact gccccgggcc

4681
tgtataccgg ataatgacgc agtgctggca gcatcagcct gaagacagac ccaacttcgc

4741
catcattttg gagaggatcg aatactgcac ccaggacccc gatgtgatca acacagctct

4801
gcccatcgaa tacggtccag tagtagaaga ggaggagaaa gtgcccatgc gccccaaaga

4861
ccccgagggg atgccacctt tgctggtgtc tccccagcct gcgaagcacg aggaggcgtc

4921
cgcagctccc cagcccgcag ccctgacggc accaggccca tcggtgaaga agcccccggg

4981
tgcgggtgcg ggcgcgggcg cgggtgcggg tgccggcccg gtgccccgag gtgcggccga

5041
tcggggccac gtgaacatgg ctttctctca gcccaaccct cccccggagc tgcacaaagg

5101
cccgggatcc agaaacaagc cgaccagcct gtggaacccc acctacggct cgtggttcac

5161
cgagaagcct gccaaaaaga cccatcctcc gccaggcgcc gagccgcagg cgcgggcagg

5221
agcggccgag ggtggctgga ccgggccggg cgcggggccc cgcagagccg aggcagcgct

5281
gctgctagag ccatcggcgc tgagcgccac catgaaggag gtgccgctgt tcaggctgcg

5341
ccacttcccc tgcggcaatg tcaactatgg ttaccagcaa cagggtctcc ccttggaagc

5401
cacagccgcg ccaggggaca ccatgctgaa aagcaagaat aaggtcaccc agccggggcc

5461
ctgagccctg tactccacta gcttctcctc ctggcggagc cggagcccac ccagagggag

5521
atggacagga tggctccacc acaaacccaa gaccaaaact ttcatttttg tgccaacttg

5581
ttttgaagtg ccacatttta aaaaaaggaa acttgtgttt ttaagatgtg ttagaaggtt

5641
ttttgagcat gggttcatct atcctctcaa aagaagaaaa tgccattctt taaaaaagaa

5701
aaaaaagcaa tcagtgcaag gcccagattg gttgcgccaa gttttcgtgc atggtctgct

5761
gtacagtccc ctaaggcttc tttccgattt ttgtgtgcgc tctgcttccg cgtagtcaga

5821
aatagctgct tccatgtctc atagggggag tcctaggtgt ttcctttgcc ttatgaatat

5881
gaaccactcg aggggcgggc gagggaacag aaataaag

By “alteration” is meant a change (increase or decrease) in the expression levels or activity of a gene or polypeptide as detected by standard art known methods such as those described herein. As used herein, an alteration includes a 5% change in expression levels, a 10% change in expression levels, preferably a 25% change, more preferably a 40% change, and most preferably a 50% or greater change in expression levels.

By “ameliorate” is meant decrease, reduce, delay diminish, suppress, attenuate, arrest, or stabilize the development or progression of a disease or pathological condition.

By “antibody” is meant an immunoglobulin (Ig) molecule produced by B lymphoid cells and having a specific amino acid sequence with an antigen binding site that specifically binds an antigen. “Antibody” may be used interchangeably herein with “immunoglobulin” or “Ig.”

Antibodies are evoked or elicited in subjects (e.g., humans, mammals, or other animals) following exposure to a specific antigen. A subject capable of generating antibodies (i.e., an immune response) directed against a specific antigen is said to be immunocompetent.

Typically, an immunoglobulin has heavy (H) chains and light (L) chains interconnected by disulfide bonds. Immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon and mu constant region genes, as well as the myriad immunoglobulin variable domain genes. There are two types of light chain, lambda (λ) and kappa (κ). There are five main heavy chain classes (or isotypes) which determine the functional activity of an antibody molecule:

IgM, IgD, IgG, IgA and IgE.

Each heavy and light chain contains a constant region (or constant domain) and a variable region (or variable domain) (see, e.g., Kindt et al. Kuby Immunology, 6.sup.th ed., W.H. Freeman and Co., page 91 (2007)). In several embodiments, the heavy and the light chain variable regions combine to specifically bind the antigen (e.g., an ALK protein or fragment thereof). Reference to “VH” refers to the variable region of an antibody heavy chain or an antigen binding fragment thereof, including Fv, scFv, dsFv or Fab. Reference to “VL” refers to the variable domain of an antibody light chain or an antigen binding fragment thereof, including Fv, scFv, dsFv or Fab.

Light and heavy chain variable regions contain a framework region (FR) interrupted by three hypervariable regions, also called complementarity-determining regions (CDRs) (see, e.g., Kabat et al., Sequences of Proteins of Immunological Interest, U.S. Department of Health and Human Services, 1991). The sequences of the framework regions of different light or heavy chains are relatively conserved within a species. The framework region of an antibody, that is the combined framework regions of the constituent light and heavy chains, serves to position and align the CDRS in three-dimensional space. In some embodiments, the spatial orientation of CDRs and FRs are as follows, from N-terminus to C-terminus: FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4.

In some embodiments, the variable region is a primate (e.g., human or non-human primate) variable region. In some embodiments, the variable region is a human variable region. In some embodiments, the variable region comprises murine (e.g., mouse or rat) CDRs and primate (e.g., human or non-human primate) framework regions (FRs). In some embodiments, the variable region comprises murine (e.g., mouse or rat) CDRs and human framework regions (FRs). In one embodiment, a variable region described herein is obtained from assembling two or more fragments of human sequences into a composite human sequence.

In some embodiments, the anti-ALK antibody or an antigen binding fragment thereof comprises a VL region selected from ALK Antibody #1 (ALK #1), ALK Antibody #2 (ALK #2), ALK Antibody #3 (ALK #3), ALK Antibody #4 (ALK #4), ALK Antibody #5 (ALK #5), ALK Antibody #6 (ALK #6), or ALK Antibody #7 (ALK #7). In some embodiments, the anti-ALK antibody VL region is selected from ALK #1. In some embodiments, the anti-ALK antibody VL region is selected from ALK #2. In some embodiments, the anti-ALK antibody VL region is selected from ALK #3. In some embodiments, the anti-ALK antibody VL region is selected from ALK #4. In some embodiments, the anti-ALK antibody VL region is selected from ALK #5. In some embodiments, the anti-ALK antibody VL region is selected from ALK #6. In some embodiments, the anti-ALK antibody VL region is selected from ALK #7.

In some embodiments, the anti-ALK antibody VL region is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to an exemplary anti-ALK antibody VL amino acid sequence as provided below:

DIQMTQSPASLAASVGETVTITCRASENIYYSLAWYQQKQGKSPQLLIYN

ANSLEDGVPSRFSGSGSGTQYSMKINSMQPEDTATYFCKQAYDVPFTFGS

GTKLEIKR

AIQMTQTTSSLSASLGDRVTISCSVSQGISNSLNWYQQKPDGTVKLLIYY

TSSLHSGVPSRFSGSGSGTDYSLTISNLEPEDIATYYCQQYSKLPLTFGA

GTKLELKR

DIVMTQSQRFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKALI

YSASYRYSGVPDRFTGSGSGTDFTLTVSNVQSEDLAEYFCQQYNSYPY

MYTFGGGTKLEIKR

DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFMNWFQQKPGQPP

KLLIYAASNQGSGVPARFSGSGSGTDFSLNIHPMEEDDTAMYFCQQSK

EVPWTFGGGTKLEIKR

DIVMTQSQREMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKALI

YSASYRYSGVPDRETGSGSGTDFTLTISNVQSEDLAEYFCQQYNSYPY

MYTFGGGTKLEIKR

DIVMTQSQKFMSTSVGDRVSITCKASQNVGTAVAWYQLKPGQSPKLLIY

SASNRFTGVPDRFTGSGSGTDFTLTISNMQSEDLADYFCQQYSSYPLTF

GSGTKLEIKR

DIVMTQSQKFMSTSVGDRVSVTCKASQNVGTNVAWYQQKPGHSPKALIYS

ASYRYSGVPDRFTGSGSGTDFTLTISNVQSEDLAEYFCQRYNSYPYMFTF

GGGTKLEIKR

In some embodiments, the anti-ALK antibody VL region is encoded by a polynucleotide that is at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to an exemplary nucleic acid sequence as provided below:

gacatccaga tgactcagtc tccagcctcc ctggctgcat ctgtgggaga aactgtcacc 60

atcacatgtc gagcaagtga gaacatttac tacagtttag catggtatca gcagaagcaa 120

gggaaatctc ctcagctcct gatctataat gcaaacagct tggaagatgg tgtcccatcg 180

aggttcagtg gcagtggatc tgggacacag tattctatga agatcaacag catgcagcct 240

gaagataccg caacttattt ctgtaaacag gcttatgacg ttccattcac gttcggctcg 300

gggacaaagt tggaaataaa acgg 324

gctatccaga tgacacagac tacatcctcc ctgtctgcct ctctgggaga cagagtcacc 60

atcagttgca gtgtaagtca gggcattagc aattctttaa actggtatca gcagaaacca 120

gatggaactg ttaaactcct gatctattac acatcaagtt tacactcagg agtcccatca 180

aggttcagtg gcagtgggtc tgggacagat tattctctca ccatcagcaa cctggaacct 240

gaagatattg ccacttacta ttgtcagcag tatagtaagc ttccgctcac gttcggtgct 300

gggaccaagc tggagctgaa acgg 324

gacattgtga tgacccagtc tcaaagattc atgtccacat cagtaggaga cagggtcagc 60

gtcacctgca aggccagtca gaatgtgggt actaatgtag cctggtatca acagaaacca 120

gggcaatctc ctaaagcact gatttactcg gcatcctacc ggtacagtgg agtccctgat 180

cgcttcacag gcagtggatc tgggacagat ttcactctca ccgtcagcaa tgtgcagtct 240

gaagacttgg cagagtattt ctgtcagcaa tataacagct atccgtacat gtacacgttc 300

ggagggggga ccaagctgga aataaaacgg 330

gacattgtgc tgacccaatc tccagcttct ttggctgtgt ctctagggca gagggccacc 60

atctcctgca gagccagcga aagtgttgat aattatggca ttagttttat gaactggttc 120

caacagaaac caggacagcc acccaaactc ctcatctatg ctgcatccaa ccaaggatcc 180

ggggtccctg ccaggtttag tggcagtggg tctgggacag acttcagcct caacatccat 240

cctatggagg aggatgatac tgcaatgtat ttctgtcagc aaagtaagga ggttccgtgg 300

acgttcggtg gaggcaccaa gctggaaatc aaacgg 336

gacattgtga tgacccagtc tcaaagattc atgtccacat cagtaggaga cagggtcagc 60

gtcacctgca aggccagtca gaatgtgggt actaatgtag cctggtatca acagaaacca 120

gggcaatctc ctaaagcact gatttactcg gcatcctacc ggtacagtgg agtccctgat 180

cgcttcacag gcagtggatc tgggacagat ttcactctca ccatcagcaa tgtgcagtct 240

gaagacttgg cagagtattt ctgtcaacaa tataacagct atccgtacat gtacacgttc 300

ggagggggga ccaagctgga aataaaacgg 330

gacattgtga tgacccagtc tcaaaaattc atgtccacat cagtaggaga cagggtcagc 60

atcacctgta aggccagtca gaatgtgggt actgctgtag cctggtatca actgaaacca 120

ggacaatctc ctaaactact gatttactcg gcatccaatc ggttcactgg agtccctgat 180

cgcttcacag gcagtggatc tgggacagat ttcactctca ccatcagcaa tatgcagtct 240

gaagacctgg cagattattt ctgccagcaa tatagcagct atcctctcac gttcggctcg 300

gggacaaagt tggaaataaa acgg 324

gacattgtga tgacccagtc tcaaaaattc atgtccacat cagtaggaga cagggtcagc 60

gtcacctgca aggccagtca gaatgtgggt actaatgtag cctggtatca acagaaacca 120

gggcactctc ctaaagcact gatttactcg gcatcctacc ggtacagtgg agtccctgat 180

cgcttcacag gcagtggatc tgggacagat ttcactctca ccatcagcaa tgtgcagtct 240

gaagacttgg cagagtattt ctgtcagcga tataacagct atccgtacat gttcacgttc 300

ggagggggga ccaagctgga aataaaacgg 330

In some embodiments, the anti-ALK antibody or an antigen binding fragment thereof comprises a VH region selected from ALK Antibody #1 (ALK #1), ALK Antibody #2 (ALK #2), ALK Antibody #3 (ALK #3), ALK Antibody #4 (ALK #4), ALK Antibody #5 (ALK #5), ALK Antibody #6 (ALK #6), or ALK Antibody #7 (ALK #7). In some embodiments, the anti-ALK antibody VH region is selected from ALK #1. In some embodiments, the anti-ALK antibody VH region is selected from ALK #2. In some embodiments, the anti-ALK antibody VH region is selected from ALK #3. In some embodiments, the anti-ALK antibody VH region is selected from ALK #4. In some embodiments, the anti-ALK antibody VH region is selected from ALK #5. In some embodiments, the anti-ALK antibody VH region is selected from ALK #6. In some embodiments, the anti-ALK antibody VH region is selected from ALK #7.