WO2009028968A1 - Cell marker of melanocyte cell lineage and uses thereof - Google Patents

Cell marker of melanocyte cell lineage and uses thereof Download PDF

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Publication number
WO2009028968A1
WO2009028968A1 PCT/NZ2008/000223 NZ2008000223W WO2009028968A1 WO 2009028968 A1 WO2009028968 A1 WO 2009028968A1 NZ 2008000223 W NZ2008000223 W NZ 2008000223W WO 2009028968 A1 WO2009028968 A1 WO 2009028968A1
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seq
nucleic acid
acid molecule
cell
peptide
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PCT/NZ2008/000223
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French (fr)
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WO2009028968A8 (en
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Peter Roderick Dunbar
Oliver Horlacher
Vaughan John Feisst
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Auckland Uniservices Limited
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Priority to EP08828507A priority Critical patent/EP2190870A4/en
Priority to AU2008293138A priority patent/AU2008293138A1/en
Publication of WO2009028968A1 publication Critical patent/WO2009028968A1/en
Publication of WO2009028968A8 publication Critical patent/WO2009028968A8/en

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    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407Specifically defined cancers
    • G01N33/5743Specifically defined cancers of skin, e.g. melanoma
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61PSPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00Antineoplastic agents
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00Medicinal preparations containing peptides

Definitions

  • the present invention relates to cell markers and in particular to cell markers of melanocyte lineage and cancer cells.
  • the invention also relates to novel targets for treatment of disorders of cells of the melanocyte lineage, and to compositions and methods for treatment of such disorders.
  • the invention has been developed primarily for the diagnosis and/or treatment of melanocyte disorders such as cancer, and more specifically melanoma. However, it will be appreciated that the invention is not limited to this particular field of use. BACKGROUND OF THE INVENTION
  • Melanoma is the most serious and aggressive form of skin cancer. However, if recognized and treated early, it is nearly 100 percent curable. If not captured early, the cancer can advance and spread to other parts of the body, where it becomes hard to treat and can be fatal. While it is not the most common skin cancer, it causes the most deaths.
  • Melanoma is a malignant tumor that originates in melanocytes.
  • Melanocytes manufacture the pigment melanin within melanosomes, which are transferred to keratinocytes to pigment the skin. All melanocyte specific genes identified to date are in some way involved in the melanosome production pathway.
  • Well known melanocyte- specific genes include melcmA, tyrosinase, trp-1, trp-2 and gp 100.
  • MelanA, gplOO and tyrosinase are genes that are currently used as targets for immunotherapy.
  • DTIC dacarbazine
  • BCNU carmustin
  • tamoxifen tamoxifen
  • cisplatin and vinblastine a drug that is administered orally.
  • temozolomide Another drug, temozolomide, can be given orally.
  • the present invention is concerned with a novel gene and its products that appear to be expressed primarily in melanocytes.
  • the present invention is also concerned with methods of modulating the expression or function of the gene and/or its products.
  • an isolated nucleic acid molecule that encodes a melanocyte-specific protein comprising a nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or functional fragments thereof.
  • the nucleic acid molecule that encodes a protein having SEQ. ID. No.3, or a functional fragment thereof.
  • an isolated nucleic acid molecule that encodes a melanocyte-specific protein, wherein the nucleic acid molecule has at least 75% sequence identity with SEQ. ID. No. 1.
  • the nucleic acid molecule has from 80% to 95% sequence identity with SEQ. ID. No. 1.
  • Nucleic acid molecules that have higher sequence identities with SEQ. ID. NO. 1, for example 80%, 85%, 90% or 95% are even more preferred.
  • nucleic acid sequence of the present invention may vary from that provided in SEQ. ID. No.l as a result of codon degeneracy (i.e. alternative codons for the same amino acid residue) or preferential codon usage if the sequence is to be expressed in different expression systems (e.g. prokaryotic, eukaryotic systems etc.).
  • a nucleic acid molecule that is complementary to a nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or fragments thereof.
  • a protein comprising a polypeptide sequence encoded by an isolated nucleic acid molecule of aspect one or aspect two.
  • a cell marker comprising a peptide or polypeptide sequence encoded by an isolated nucleic acid molecule of aspect one or aspect two, or part thereof.
  • a cell marker comprising a peptide or polypeptide sequence comprising SEQ ID No. 3.
  • the cell marker is a skin cell marker such as, for example, a melanocyte cell marker.
  • the skin cell is a melanocyte.
  • the cell marker is a cell marker for skin-related neoplastic conditions such as skin cancer. More preferably the neoplastic condition is melanoma.
  • the condition may also be a disorder of pigmentation resulting from, for example, abnormal localisation, growth, or function of melanocytes.
  • an antibody that binds to the peptide or polypeptide sequence encoded by a nucleic acid molecule of aspect one or aspect two, or part thereof, or to a protein comprising SEQ ID No. 3, or part thereof.
  • the antibody is a monoclonal antibody or a functional fragment thereof.
  • the antibody is a polyclonal antibody or a functional fragment thereof.
  • antibody includes functional fragments of antibodies, derived by enzymatic means or recombinant expression.
  • a pharmaceutical composition comprising an antibody according to the seventh aspect, optionally in combination with a pharmaceutically acceptable carrier.
  • a vector comprising a nucleic acid sequence set forth in any one of aspects one to three, or a part thereof, operatively linked to a promoter.
  • the vector can be selected from an expression vector commonly used for in vitro protein expression in prokaryotic or eukaryotic cells, or vectors for introducing nucleic acid sequences into mammalian cells or vectors for mammalian gene therapy or vaccination.
  • a prokaryotic or eukaryotic cell comprising the expression vector according to the ninth aspect.
  • the prokaryotic cell is a bacterial cell or a fungal cell.
  • the eukaryotic cell is selected from a mammalian cell, an avian cell, an amphibian cell, a reptilian cell or an insect cell.
  • nucleic acid molecule of aspect one or aspect two a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or part thereof, or a protein comprising said peptide or polypeptide, as a marker of a melanocyte cell lineage.
  • an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or part thereof, or a protein comprising said peptide or polypeptide, for identifying melanocyte cell lineage.
  • the identification of cell lineage can be conducted by a number of well known techniques, including for example FACS, ELISA, RIA, Western blot, cytometric bead array, SISCARPA , and the like.
  • nucleic acid molecule comprising a nucleic acid molecule of aspect one or aspect two, or part thereof, or a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or part thereof, or a protein comprising said peptide or polypeptide, or a protein having SEQ ID No.3, or part thereof, or an antibody that specifically binds to said peptide or polypeptide and/or said protein, in the diagnosis and/or detection of a skin cancer.
  • nucleic acid molecule of aspect one or aspect two or part thereof or an inhibitory or interfering RNA or DNA sense or antisense sequence, or an antibody that specifically binds to a polypeptide encoded by a nucleic acid of aspect one or aspect two, or part thereof, or a protein comprising said polypeptide in the preparation or manufacture of a medicament for the treatment of a skin cancer or disorders associated with melanoma and/or disorders of pigmentation, and/or abnormal function, localisation or growth of melanocytes.
  • a method of diagnosing and/or treating a skin cancer comprising the step of administering to a subject in need of said treatment an effective amount of an inhibitory or interfering RNA or DNA sense or antisense sequence capable of blocking or inhibiting expression of a nucleic acid molecule of aspect one or aspect two, or part thereof, or an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or part thereof, or a protein comprising said peptide or polypeptide, or a protein having SEQ. ID No.3.
  • the skin cancer is melanoma.
  • a method of screening for the presence of a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, in a sample comprising: a) contacting a biological sample with a nucleic acid having a sequence that is complementary to nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof; and b) determining whether the nucleic acid binds to a nucleic acid molecule in the sample.
  • a method of screening for the presence of a peptide or polypeptide or part thereof, encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, in a sample comprising: a) contacting a biological sample with an antibody that specifically binds to the peptide or polypeptide, or part thereof; and b) determining whether the antibody binds to the peptide or polypeptide, or part thereof, in the sample.
  • a method of screening for the presence of a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, and at least one other nucleic acid molecule which codes for a cell marker commonly used to identify cells of melanocyte lineage in a sample comprising: a) contacting a biological sample with i) a nucleic acid molecule having a sequence that is complementary to nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No.
  • nucleic acid molecules having a sequence that is complementary to the at least one other nucleic acid molecule or part thereof; and b) determining whether the nucleic acid molecules bind to the nucleic acid molecules in the sample.
  • a method of screening for the presence of a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, and at least one other polypeptide which is a cell marker commonly used to identify cells of melanocyte lineage in a sample comprising: a) contacting a biological sample with i) an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, and ii) an antibody that specifically binds to the at least one other polypeptide; and b) determining whether the antibodies bind to their corresponding polypeptides in the sample.
  • the cell marker commonly used to identify cells of melanocyte lineage may be selected from for example, melanA, gplOO, tyrosinase, trp-1 and trp-2. It will be understood however, that any other markers that identify melanocyte cell origin can also be used in conjunction with the present invention.
  • the use of the cell marker encoded by any one of SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8 in a panel of other markers is advantageous since not all cancerous cells express traditional markers such as gplOO or melanA, and the like, which are typically used in methods for screening for melanoma. Inclusion of an additional marker such as that of the present invention significantly enhances the diagnostic power of the diagnostic methods used.
  • a method of diagnosing and/or detecting skin cancer or skin condition comprising: a) contacting a biological sample with a nucleic acid having a complementary sequence to nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof; and b) detecting localisation of the nucleic acid as an indicator of the presence (and/or type) of skin cancer or skin condition.
  • a method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof; and b) detecting localisation of the antibody as an indicator of the presence (and/or type) of skin cancer or skin condition.
  • a method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with a nucleic acid having a complementary sequence to nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ.
  • nucleic acid molecules selected from the group comprising, but not limited to melanA, gplOO, tyrosinase, trp-1 and trp-2, or parts thereof; and b) determining localisation of the nucleic acids as an indicator of the presence (and/or type) of skin cancer or skin condition.
  • a method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, and at least one other antibody that binds to a polypeptide encoded by melanA, gplOO, tyrosinase, trp-1 and trp-2, or parts thereof, and b) determining localisation of the antibodies as an indicator of the presence (and/or type) of skin cancer or skin condition.
  • a method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with a panel of nucleic acid molecules or parts thereof, comprising melanA, gplOO, tyrosinase, trp-1 and trp-2 and a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof; and b) determining localisation of the nucleic acid molecules as an indicator of the presence (and/or type) of skin cancer or skin condition.
  • a method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with a panel of antibodies that bind specifically to melanA, gplOO, tyrosinase, trp-1 and trp-2 and a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof; and b) determining localisation of the antibodies as indicator of the presence (and/or type) of skin cancer or skin condition.
  • the biological sample used in the method of diagnosing skin cancer is selected from the group consisting of a tissue biopsy, a biological fluid and a surgical specimen. It will be understood, however, that the diagnosis and/or detection of skin cancer with nucleic acid molecules and antibodies of the present invention may also be conducted in vivo or ex vivo.
  • the nucleic acid molecules or antibodies used in the method of screening or diagnosis are tagged with a visible or detectable marker to permit visual inspection or measurement/detection.
  • the tag is preferably selected from a group consisting of a fluorescent dye, an isotope, an enzyme (e.g. peroxidase or alkaline phosphatase), a chemical moiety (e.g. biotin) that binds another labelled ligand (e.g. avidin) with high affinity.
  • the skin cancer to be screened, diagnosed or treated is melanoma.
  • the melanoma can be in the form of a cutaneous melanoma, a melanoma of the nail bed, a melanoma of the eye or a mucosal melanoma.
  • the skin cancer to be screened, diagnosed or treated may be of metastatic origin.
  • the skin condition may be a disorder of pigmentation, and/or abnormal function, localisation or growth of melanocytes.
  • a method of modulating expression of genes associated with skin cancer or skin condition comprising contacting a cell with a short interfering nucleic acid molecule directed against a nucleic acid sequence selected from
  • SEQ. ID. No. 1 SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ.
  • the short interfering nucleic acid molecule is selected from a group consisting of short interfering RNA (siRNA), double stranded RNA, micro RNA and short hairpin DNA.
  • siRNA short interfering RNA
  • double stranded RNA double stranded RNA
  • micro RNA micro RNA
  • short hairpin DNA short interfering RNA
  • a method of modulating expression of genes associated with skin cancer or skin condition comprising contacting the cells with an antisense nucleic acid molecule directed against a nucleic acid sequence selected from
  • SEQ. ID. No. 1 SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof.
  • the skin cancer is melanoma.
  • nucleic acid molecule comprising a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, or an inhibitory or interfering RNA or DNA sense or antisense sequence, or an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, or a protein comprising said peptide or polypeptide, in the treatment of disorders associated with melanoma and/or disorders of pigmentation, and/or abnormal function, localisation or growth of melanocytes.
  • the disorders of pigmentation include hyperpigmentation disorders such as melasma, cafe au lait macules, drug-induced hyper-pigmentation and phototoxic reactions or hypo- pigmentation disorders such as vitiligo.
  • hyperpigmentation disorders such as melasma, cafe au lait macules, drug-induced hyper-pigmentation and phototoxic reactions or hypo- pigmentation disorders such as vitiligo.
  • autoimmune vitiligo Ogg GS, Dunbar PR, Romero P, Chen JL, Cerundolo V (1998) High frequency of skin-homing melanocyte-specific cytotoxic T lymphocytes in autoimmune vitiligo. Journal of Experimental Medicine 188:1203-8). More preferably, the disorders of pigmentation is selected from hypo- pigmentation and/or hyper-pigmentation.
  • a method of modulating expression of genes associated with changes in skin pigmentation or cosmetic lightening or darkening of skin tone comprising contacting a cell with an inhibitory or interfering RNA or DNA, sense or antisense, sequence directed against a nucleic acid molecule of aspect one or aspect two.
  • the nucleic acid molecules and antibodies of present invention may be formulated into pharmaceutical preparations by any number of processes well known in the art and may include injectable, topical, oral, slow release and other suitable dosage forms and preparations.
  • the present invention is suitable for the diagnosis and/or treatment of skin cancers, in particular melanoma.
  • LOCI 46481 is used for convenience to describe the genomic locus LOC 146481.
  • Novel nucleic acid sequences of the present invention in addition to being allocated SEQ ID Nos. may also be referred to as "SHML” sequences (Specific for Human Melanocyte Lineage). It will be understood that the acronym is merely a convenient designation and should not be construed to limit the nucleic acid or the protein to human origin only.
  • the present invention encompasses both mammalian and non-mammalian species SHML.
  • SHML mRNA “SHML gene”, “SHML transcript” and “SHML protein” may be used interchangeably with specific SEQ ID nos. and are intended to describe the nucleic acid, mRNA and protein sequences of the present invention.
  • nucleotide As used in the context of the present invention, are intended to encompass a gene, DNA, ssDNA, cDNA, synthetic DNA, RNA, genomic sequences and derivatives thereof.
  • peptide and “polypeptide” as used in the context of the present invention are intended to encompass peptides and fragments of polypeptides or proteins which comprise an amino acid sequence encoded by SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or parts thereof. Such sequences may be detectable by an antibody raised against a peptide encoded by SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof, such as for example SEQ ID No. 3 or part thereof.
  • treatment covers any treatment of a disease and/or condition in an animal, particularly a human, and includes:
  • an “antibody” or “antibodies” includes reference to all the various forms of antibodies, including but not limited to: full antibodies (e.g. having an intact Fc region), including, for example, monoclonal antibodies; antigen-binding antibody fragments, including, for example, Fv, Fab, Fab' and F(ab') 2 fragments; humanized antibodies; human antibodies (e.g., produced in transgenic animals or through phage display); single domain antibodies and immunoglobulin-derived polypeptides produced through genetic engineering techniques. Unless otherwise specified, the terms "antibody” or “antibodies” and as used herein encompasses both full antibodies and antigen-binding fragments thereof.
  • the treatments described herein can be administered by oral or parenteral routes, including intravenous, intramuscular, intraperitoneal, subcutaneous, rectal and topical administration, and inhalation.
  • oral administration the treatments will generally be provided in the form of tablets or capsules or as an aqueous solution or suspension.
  • Tablets for oral use may include the active ingredient mixed with pharmaceutically acceptable excipients such as inert diluents, disintegrating agents, binding agents, lubricating agents, sweetening agents, flavouring agents, colouring agents and preservatives.
  • pharmaceutically acceptable excipients such as inert diluents, disintegrating agents, binding agents, lubricating agents, sweetening agents, flavouring agents, colouring agents and preservatives.
  • “pharmaceutically acceptable carrier” includes any material which, when combined with an active ingredient, allows the ingredient to retain biological activity and is non-reactive with the subject's immune system. Examples include, but are not limited to, any of the standard pharmaceutical carriers such as a phosphate buffered saline solution, water, emulsions such as oil/water emulsion, and various types of wetting agents. Preferred diluents for aerosol or parenteral administration are phosphate buffered saline or normal (0. 9%) saline.
  • Figure 1 The PCR products derived from human melanocyte cDNA encoding SHML Sequence 1. AU sequences are shown 5'- 3'.
  • B PCR product 2 - SEQ ID No.
  • 10 - shows 546bp of the sequence of the PCR product generated from human melanocyte cDNA with forward primer 527F (5'- TGGTCAGGATGGAGGGGAAG-3') and reverse primer 1145R (5'- GCACCCAGCTCAAGCCTCAT-3 '); C) Alignment of two PCR products in A) and B), which overlap by lObp, to make
  • SEQ. ID. No. 3 is the protein sequence encoded by the underlined portion of SEQ. ID. No. 2.
  • Figure 2 Excerpt of the GenBank entry for the human FRG2 gene sequence
  • Figure 3 Alignment of SHML protein sequence (SEQ. ID. No. 3) with FRG2 protein sequence (by Needleman-Wunsch global alignment, Geneious software, www.geneious.com). Potential nuclear localisation signals are boxed, and a potential protein kinase C phosphoryation site is underlined.
  • FIG. 4 Expression of SHML, tyrosinase & melanA relative to the house-keeping gene HPRT in cDNA from human tissues, cell lines, and primary cell cultures. Expression of these three genes was quantified with quantitative RT-PCR relative to the housekeeping gene HPRT, which was expressed in all samples. SHML expression was detected in human skin, which contain melanocytes, and also in cultured human melanocytes, but not cultured human dermal fiboblasts. The melanocyte-associated gene tyrosinase and melanA were also expressed in human skin and melanocytes, but not dermal fibroblasts.
  • siRNAs targeting SHML mRNA achieved approximately 70% knockdown of SHML expression, similar to the level of knockdown seen with previously- validated siRNAs targeting tyrosinase mRNA.
  • 5OnM siRNA had similar effects, but InM siRNAs were less effective. These data indicate the siRNAs used were capable of significantly knocking down SHML mRNA expression at both the 1OnM and 5OnM doses. Data shown are the average of triplicate measurements, with error bars representing the standard error of the mean.
  • Figure 6 siRNAs targeting SHML gene expression
  • FIG. 6 The two siRNA sequences used to knock down SHML expression in Figure 6 are shown, along with the positions of the sequences they target in the SHML sequence (bold and underlined in SEQ. ID. No. 1 as shown)
  • Figure 7 Alternate transcripts coding for SHML.
  • A)-D) Four predicted alternate transcripts are shown that are capable of encoding SHML protein (SEQ. ID. No. 3), each full length from transcription initiation site (TCATTCTT, nucleotides 1-8 in each transcript) to poly- A tail start. The coding sequence is underlined in each sequence. Three polymorphic sites are highlighted in each sequence by use of a bold capitalised A or G.
  • the first 360bp of each sequence, and the sequences 3' to the regions shown here, have been omitted, since they are identical between the transcripts.
  • Figure 8 Features of the SHML promoter region.
  • TTATGTAA 115..122 cAMP Response Element
  • TGAGGTTA cAMP Response Element
  • CACATG Putative Mitf binding site
  • the present invention is based on a surprising observation that an uncharacterised gene in the human genome encodes a protein that is present in cells of melanocy e lineage, but not other cells.
  • an uncharacterised gene in the human genome encodes a protein that is present in cells of melanocy e lineage, but not other cells.
  • novel nucleic acid sequence that encodes the novel, cell-specific protein, provided herein is designated
  • the protein-encoding open reading frame (ORF) from SEQ. ID. No. 1 mRNA is the nucleotide sequence shown below (SEQ. ID. No. 2): SEQ. ID. No. 2
  • SEQ. ID. No. 3 This ORF is one of several possible ORFs in SEQ. ID. No. 1, but based on the present findings of the encoded protein's high homology to another human protein, as described below, SEQ. ID. No. 2 was identified as the protein coding sequence.
  • the protein encoded by SEQ. ID. No. 2 has the following amino acid sequence (SEQ. ID. No. 3):
  • SEQ. ID. No. 3 has significant homology to another known protein, called FRG2 (FSHD region gene 2), the sequence of which is given in Figure 2, along with other information on the gene encoding FRG2 protein.
  • FRG2 is a gene implicated in facioscapulohumeral muscular dystrophy (T. Rijkers et al, FRG2, an FSHD candidate gene, is transcriptionally up-regulated in differentiating primary myoblast cultures of FSHD patients. J. MedGenet. 2004;41; 826-836).
  • Alignment of the SEQ. ID. No. 3 with FRG2 protein sequence is shown in Figure 3. In this alignment, 50 of 113 amino acids in SEQ. ID. No. 3 protein are identical to those in FRG2, for 44% overall homology.
  • SEQ. ID. No. 3 has a homologous protein sequence for only the second sequence at amino acids 70-73 (sequence KQHR).
  • SEQ. ID. No. 3 does have a potential nuclear localisation signal (sequence LKKKLKS) that is not present in FRG2 (using PredictNLS online http://cubic.bioc.columbia.edu/cgi/var/nair/resonline.pl). Based on these findings it is therefore likely that the SEQ. ID. No. 3 protein will localise to the nucleus of the cell after translation, as does FRG2.
  • the sequence SNKL at amino acids 47-50 in the SEQ. ID. No. 3 protein is a potential protein kinase C (PKC) phosphorylation site, implicating PKC as a regulator of the protein's function.
  • PKC protein kinase C
  • the SEQ. ID. No. 3 protein is thus potentially capable of post- translational modification by phosphorylation at this site.
  • MITF microophthalmia-associated transcription factor
  • CREB cAMP-responsive element binding protein
  • the genomic locus LOC146481 had been predicted by NCBI to encode mRNAs (XR_017714.1, XR_017753.1, and XR_041323.1), different from that identified herein as SEQ. ID. No. 1. These predicted mRNAs (XR_017714.1, XRJH7753.1, and XR_041323.1), had been predicted to encode a protein different from SEQ. ID. No. 3 described herein (predicted hypothetical protein XPJ)01723191.1).
  • GenBank National Institutes of Health Mammalian Gene Collection project (NIH MGC) also differs from SEQ. ID. No. 1, and has several reading frames.
  • SEQ. ID. No. 1 of the present invention In analysing SEQ. ID. No. 1 of the present invention, it was found that one of several open-reading frames encoded a protein with strong homology to another human protein, FRG2. Based on analytical and comparative studies described above, particularly the recognition that the sequence was restricted to cells of the melanocytic lineage and, on the basis of strong homology to another protein, (that only one of the open-reading frames present in SEQ. ID. No. 1 was likely to encode protein) the present invention provides a novel nucleotide sequence, SEQ. ID. No.l, the mRNA sequence included therein, SEQ. ID. No. 2, and the corresponding protein sequence, SEQ. ID. No. 3. The restriction of the sequences to cells of the melanocytic lineage, indicates a function related to the specialised properties of such cells, as described below. Expression of SHML transcripts in human tissues and cells
  • the gene and its corresponding protein will therefore have value as a diagnostic marker for confirmation of diagnosis of cancers such as melanoma, a marker of a melanocyte cell lineage, as a therapeutic drug target, for example as a target for immunotherapy of melanoma or a drug target for melanoma or disorders of pigmentation. Its corresponding antibody will also have value as a diagnostic tool or as a treatment/therapy for melanoma in its various forms and for disorders associated with melanoma and/or disorders of pigmentation. Functional roles of SHML protein
  • DAGI melanoma cell line
  • siRNAs targeting SHML mRNA both siRNAs shown in Fig 6
  • control siRNAs targeting the melanocyte marker tyrosinase were exposed to siRNAs targeting SHML mRNA.
  • DAGI melanoma cell line
  • siRNAs targeting SHML mRNA both siRNAs shown in Fig 6
  • control siRNAs targeting the melanocyte marker tyrosinase was exposed to siRNAs targeting SHML mRNA (both siRNAs shown in Fig 6), as well as control siRNAs targeting the melanocyte marker tyrosinase.
  • Fig 5 This was equivalent to the knock down in tyrosinase mRNA concentrations in the same experiment, carried out with siRNAs that had been previously validated.
  • DAGI cells with and without SHML mRNA knockdown were subjected to whole genome microarray analysis, to detect gene modulated by SHML.
  • Wnt proteins interact with a cell surface receptor complex consisting of Frizzled and LRP5/6, resulting in stabilisation of cytoplasmic ⁇ -catenin.
  • ⁇ -catenin accumulates in the cytoplasm and moves to the nucleus. Once in the nucleus ⁇ -catenin interacts with the LEF/TCF family of transcription factors to activate transcription of TCF/LEF target genes.
  • DKKl is able to inhibit Wnt signalling at the cell surface by binding to LRP5/6 component of the Wnt receptor complex. The complex is endocytosed upon DKKl binding, thereby blocking the ability of Frizzled to send the Wnt signal upon binding of Wnt.
  • Wnt signalling is crucial in development, differentiation, and pigmentation. Wnt signalling is required to maintain melanocyte precursor cells in a stem cell like state during development. Wnt signalling has been shown to control pigmentation by activation of Mitf-M transcription via the TCF/LEF1 binding site in the Mitf-M promoter. Wnt signalling in melanocytes results in the ⁇ -catenin/TCF/LEF complex increasing transcription of Mitf-M. Downstream of Mitf-M the pigmentation pathway is activated and melanosomes are produced. (2-4)
  • SHML protein therefore appears to be a negative regulator of DKKl expression. Reduction in SHML mRNA levels resulted in increased DKKl mRNA expression levels, as demonstrated herein.
  • SHML protein is a putative transcription factor and may regulate DKKl mRNA levels via interaction with the DKKl promoter.
  • SHML protein is a melanocyte-specific regulator of the Wnt signalling pathway, which has been shown to be required for melanocyte development, differentiation and pigmentation.
  • the tissue specificity of SHML protein expression enables systemic drug treatment with a tissue specific effect on Wnt signalling.
  • siRNAs were used to successfully knock down expression of SHML mRNA in melanoma cells by at least 60%, with subsequent effects on the transcription of other genes, notably DKKl.
  • the location of the sequences successfully targeted by siRNAs are shown in Fig 6, along with the siRNA sequences. These sequences are located at residues 552-570, and 637-655 of the SEQ. ID. No. I 5 and were targeted by siRNAs 293438 and 293439 (provided by Applied Biosystems/Ambion, Austin, TX, USA).
  • the siRNAs have similar efficacy when used individually as when combined.
  • transcripts include the lOObp additional sequence shown in transcripts 2 and 4 (SEQ. ID. No. 5 and SEQ. ID. No. 7) because RT-PCR of cDNA from cells of melanocytic origin using primers that span this region of cDNA occasionally produce two bands that differ in size by lOObp (data not shown).
  • SNPs Single Nucleotide Polymorphisms
  • allelic variants of all 4 alternate transcripts are possible, though none of these affect the encoded protein, because they are located in the untranslated regions of each mRNA.
  • SNP # 11647911 is a C/T polymorphism transcript start site, as shown at position 4018. This is not predicted to be a site involved in transcription factor binding or transcription initiation, but it is still possible that it will affect the transcription of the gene in different individuals, potentially affecting melanocyte structure or function.
  • novel SHML protein described herein, or parts thereof, represents a new and useful target for diagnosis and treatment of skin and other conditions that are caused or mediated by abnormal melanocyte function, growth, proliferation and/or localisation.
  • the active agents described herein including anti-sense and sense nucleic acid approaches, and antibodies, to manipulating expression of the SHML protein can be applied to both diagnostic and therapeutic uses in the treatment of melanocyte-mediated disorders, the most important of which is skin cancer such as melanoma.
  • cosmetic applications are also contemplated such as alteration of skin and hair pigmentation, masking or removal of skin blemishes and the like.
  • Manipulation of regulatory processes within melanocytes has been clearly demonstrated herein using siRNAs that modulate expression of SHML.
  • the structure of the gene and its regulatory regions, and the protein sequence, provided herein enable other known therapeutic and diagnostic approaches to be adopted for manipulating the expression and/or function of
  • Seed Cascade melanocytes (catalogue # C-024-5C, Cascade Biologies Inc. 1341 SW Custer Drive, Portland OR 97219, USA, ph 503 292 9521) at a density of 5x10 3 cells/cm 2 in a 25 cm 2 flask with Cascade medium 254 (cat # M254-500) with PMA free melanocyte supplement (cat # S-015-5C).
  • DAGI Cell Culture Thaw vial of 0.5 million cells in a 37°C water bath. Open vial in a laminar flow hood and resuspend cell pellet using a ImL pipette. Transfer cells to a 15mL tube then add 1OmL RPMIl 640/10% FBS/lxPSGCpenicillin/streptomycin/glutamate). Mix cells then centrifuge for 5min at 18Og. Remove supernatant, add 5mL RPMI1640/10% FBS/lxPSG, resuspend cells and transfer to a 25 cm 2 flask. Incubate at 37°C/5%CO 2 for 24 hours then replace the media and remove dead cells. Change media every 2-3 days and passage 1:2 whenever flask becomes confluent. Passage using 2x trypsin.
  • RNAniix l ⁇ L l Ox RT buffer
  • siRNA & LF2000 mixes & incubate at room temperature for 20min.
  • Microarray Information Chips used - Affymetrix Human Genome Ul 33 Plus 2.0 Array Genechip Users protocol - http://www.affymetrix.com/support/technical/manual/expression_manual.affx Used as protocol for Genechip use from RNA to producing expression data
  • EXAMPLE 2 Determination of tissue expression specificity of the nucleic acid encoding SHML in humans using quantitative real time PCR.
  • SHML mRNA levels were measured by quantitative real time PCR (qPCR) using the Taqman specific assay ID # HsO139O151_ml. Since SHML was suspected to be a melanocyte specific gene, expression of two known melanocyte specific genes, tyrosinase and melan ⁇ , were also measured using Applied Biosystems Taqman assays, ID # HsOOl 65976_ml & HsOO924233_ml respectively. All qPCR reactions were 45 cycles, triplicates with IOng of each tissue cDNA.
  • SHML mRNA was also tested in normal human melanocytes (Cascade Biologies), samples of normal human skin and melanoma tumor-infiltrated lymph nodes (TILNs) (obtained from consenting patients), and a number of melanoma cell lines, obtained from collaborating research groups.
  • TILNs tumor-infiltrated lymph nodes
  • SHML mJRNA was shown to be expressed in skin and at a higher level in normal human melanocytes. SHML mRNA was also expressed in most melanoma cell lines including MZ2 where no other markers of melanocytic origin were expressed.
  • EXAMPLE 3 Sequencing of the nucleic acid encoding SHML in normal human melanocytes
  • PCR fragments of the nucleic acid sequence encoding SHML were generated from cDNA synthesized using RNA extracted from normal human melanocytes
  • the resulting PCR product was gel purified using the Qiagen Qiaex II Gel
  • PCR product was sequenced using the PCR primers, at 5 ⁇ M, with approximately 50ng of PCR product per reaction, on a
  • siRNAs specific for SHML can be used to knockdown SHML mRNA levels as in the melanoma cell line DAGI.
  • RNA from the siRNA knockdown can be used for microarray experiments. RNA is extracted using the Qiagen Rneasy Mini kit (Qiagen catalogue #74104). Microarray analysis of the RNA generated from these knockdowns can be done using the Affymetrix Ul 33 plus
  • SHML mRNA was found to be expressed in many melanoma cell lines and tumour samples, but was absent from nearly all normal human tissues.
  • Commercial cDNA libraries were sourced from volunteers by the respective companies and information on these donors and tissue processing is available on the company websites; normal human skin and melanoma tumor-infiltrated lymph nodes were sourced from consenting volunteers undergoing plastic surgery and lymph node resection respectively, under appropriate ethics committee oversight, and part of each sample was snap frozen in liquid nitrogen as soon as practicable and stored at -80°C until RNA extraction.
  • SHML mRNA was also switched on in skin and some neural samples.
  • SHML mRNA was found to be expressed in melanocytes, the normal cells that melanoma develops from, and which are found in skin and some neural tissue. Indeed, the expression pattern of SHML mRNA in human cell lines and tissues mirrors other genes that are only switched on in melanocytes. This finding made it highly likely that the gene is specific to cells of the melanocyte lineage, and may even play a role in some of the unique functions of these cells, such as pigmentation.
  • EXAMPLE 4 Expression of SHML protein
  • the nucleic acid sequence encoding SHML is amplified from a cDNA template using PCR and cloned into expression vectors for protein expression in E. coli, yeast and mammalian cells. The confirmed plasmid is then transfected into the appropriate cell line/cells and expression of the protein can be induced.
  • Recombinant SHML protein is purified from these cellular sources by the use of tags attached to the protein, that are encoded in the expression vector.
  • peptide Approximately lOmg of peptide is synthesized for the antibody production. The peptide is analyzed by mass spectral and HPLC analyses to ensure sequence integrity and purity prior to conjugation. The peptide is then conjugated to KLH or BSA (2-3mg). The peptide-protein conjugate is purified by gel filtration and freeze dried. The remaining unconjugated peptide is supplied. Immunization and Sera Collection:
  • the conjugated peptide is injected subcutaneously at multiple sites.
  • the initial immunization is given in Complete Freund's Adjuvant with all subsequent immunizations given in Incomplete Freund's Adjuvant.
  • the animals are bled at intervals to ascertain the titer of the antiserum. Antisera are used unpurified.
  • Immunization/Bleed Protocol A detailed immunization and bleeding schedule is provided below:

Abstract

The present invention relates to a novel protein that is a marker of melanocyte cell lineage and cancer cells, and to nucleic acids encoding the novel protein. The invention also relates to treatment of disorders of cells of the melanocyte lineage, and to compositions and methods for treatment of such disorders.

Description

CELL MARKER OF MELANOCYTE CELL LINEAGE AND USES THEREOF
TECHNICAL FIELD
The present invention relates to cell markers and in particular to cell markers of melanocyte lineage and cancer cells. The invention also relates to novel targets for treatment of disorders of cells of the melanocyte lineage, and to compositions and methods for treatment of such disorders.
The invention has been developed primarily for the diagnosis and/or treatment of melanocyte disorders such as cancer, and more specifically melanoma. However, it will be appreciated that the invention is not limited to this particular field of use. BACKGROUND OF THE INVENTION
Any discussion of the prior art throughout the specification should in no way be considered as an admission that such prior art is widely known or forms part of common general knowledge in the field.
Melanoma is the most serious and aggressive form of skin cancer. However, if recognized and treated early, it is nearly 100 percent curable. If not captured early, the cancer can advance and spread to other parts of the body, where it becomes hard to treat and can be fatal. While it is not the most common skin cancer, it causes the most deaths.
Melanoma is a malignant tumor that originates in melanocytes. Melanocytes manufacture the pigment melanin within melanosomes, which are transferred to keratinocytes to pigment the skin. All melanocyte specific genes identified to date are in some way involved in the melanosome production pathway. Well known melanocyte- specific genes include melcmA, tyrosinase, trp-1, trp-2 and gp 100. MelanA, gplOO and tyrosinase are genes that are currently used as targets for immunotherapy.
Treatment at the early stages of melanoma is promising. Most people with thin, localized melanomas are cured by appropriate surgery. Early detection still remains the best weapon in fighting skin cancer and the cure rate continues to rise.
More treatments are becoming available for more advanced disease. Research has produced a greater understanding of melanoma, leading to the development of new drugs. A number of drugs that are active in fighting cancer cells are being used to treat melanoma, and are either administered alone or in combinations. Currently, dacarbazine (DTIC), given by injection, is the only chemotherapy approved by the FDA. DTIC may be combined with carmustin (BCNU) and tamoxifen, or with cisplatin and vinblastine. Another drug, temozolomide, can be given orally. Unfortunately, to date, the response of melanomas to chemotherapy has been limited, but a great deal of research into new drugs and new approaches is being carried out.
There is therefore a need not only for novel treatments but also for novel targets that may be used to develop alternative approaches to treatment of cancers such as melanoma, and other skin conditions which involve melanocytes, such as skin, mole, freckle and pigmentation disorders, and further modulation of melanocyte growth, localisation, survival and function. Further, there is a need for treatments that target melanocytes and conditions associated with abnormal melanocyte growth, localisation and/or function.
It is an object of the present invention to overcome or ameliorate at least one of the disadvantages of the prior art, or to provide a useful alternative.
SUMMARY OF THE INVENTION
The present invention is concerned with a novel gene and its products that appear to be expressed primarily in melanocytes. The present invention is also concerned with methods of modulating the expression or function of the gene and/or its products.
In a first aspect, there is provided an isolated nucleic acid molecule that encodes a melanocyte-specific protein, comprising a nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or functional fragments thereof.
Preferably, the nucleic acid molecule that encodes a protein having SEQ. ID. No.3, or a functional fragment thereof.
In a second aspect there is provided, an isolated nucleic acid molecule that encodes a melanocyte-specific protein, wherein the nucleic acid molecule has at least 75% sequence identity with SEQ. ID. No. 1. Preferably the nucleic acid molecule has from 80% to 95% sequence identity with SEQ. ID. No. 1.
Nucleic acid molecules that have higher sequence identities with SEQ. ID. NO. 1, for example 80%, 85%, 90% or 95% are even more preferred.
The nucleic acid sequence of the present invention may vary from that provided in SEQ. ID. No.l as a result of codon degeneracy (i.e. alternative codons for the same amino acid residue) or preferential codon usage if the sequence is to be expressed in different expression systems (e.g. prokaryotic, eukaryotic systems etc.). In a third aspect, there is provided a nucleic acid molecule that is complementary to a nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or fragments thereof. In a fourth aspect, there is provided a protein comprising a polypeptide sequence encoded by an isolated nucleic acid molecule of aspect one or aspect two.
In a fifth aspect, there is provided a cell marker comprising a peptide or polypeptide sequence encoded by an isolated nucleic acid molecule of aspect one or aspect two, or part thereof. In a sixth aspect, there is provided a cell marker comprising a peptide or polypeptide sequence comprising SEQ ID No. 3. Preferably, the cell marker is a skin cell marker such as, for example, a melanocyte cell marker. Preferably the skin cell is a melanocyte. Even more preferred is that the cell marker is a cell marker for skin-related neoplastic conditions such as skin cancer. More preferably the neoplastic condition is melanoma. However, the condition may also be a disorder of pigmentation resulting from, for example, abnormal localisation, growth, or function of melanocytes.
In a seventh aspect, there is provided An antibody that binds to the peptide or polypeptide sequence encoded by a nucleic acid molecule of aspect one or aspect two, or part thereof, or to a protein comprising SEQ ID No. 3, or part thereof. Preferably, the antibody is a monoclonal antibody or a functional fragment thereof.
Alternatively, the antibody is a polyclonal antibody or a functional fragment thereof. It will be understood that the term "antibody", as used in the context of the present invention, includes functional fragments of antibodies, derived by enzymatic means or recombinant expression. In an eighth aspect, there is provided a pharmaceutical composition comprising an antibody according to the seventh aspect, optionally in combination with a pharmaceutically acceptable carrier.
In a ninth aspect, there is provided a vector comprising a nucleic acid sequence set forth in any one of aspects one to three, or a part thereof, operatively linked to a promoter.
Preferably, the vector can be selected from an expression vector commonly used for in vitro protein expression in prokaryotic or eukaryotic cells, or vectors for introducing nucleic acid sequences into mammalian cells or vectors for mammalian gene therapy or vaccination.
In a tenth aspect, there is provided a prokaryotic or eukaryotic cell comprising the expression vector according to the ninth aspect. Preferably, the prokaryotic cell is a bacterial cell or a fungal cell.
Preferably, the eukaryotic cell is selected from a mammalian cell, an avian cell, an amphibian cell, a reptilian cell or an insect cell.
In another aspect, there is provided the use of a nucleic acid molecule of aspect one or aspect two, a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or part thereof, or a protein comprising said peptide or polypeptide, as a marker of a melanocyte cell lineage.
In yet another aspect, there is provided use of a protein having SEQ ID No.3, or part thereof, as a marker of a melanocyte cell lineage.
In another aspect, there is provided the use of an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or part thereof, or a protein comprising said peptide or polypeptide, for identifying melanocyte cell lineage.
The identification of cell lineage can be conducted by a number of well known techniques, including for example FACS, ELISA, RIA, Western blot, cytometric bead array, SISCARPA , and the like.
In another aspect, there is provided a use of a nucleic acid molecule comprising a nucleic acid molecule of aspect one or aspect two, or part thereof, or a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or part thereof, or a protein comprising said peptide or polypeptide, or a protein having SEQ ID No.3, or part thereof, or an antibody that specifically binds to said peptide or polypeptide and/or said protein, in the diagnosis and/or detection of a skin cancer.
In another aspect, there is provided the use of a nucleic acid molecule of aspect one or aspect two or part thereof, or an inhibitory or interfering RNA or DNA sense or antisense sequence, or an antibody that specifically binds to a polypeptide encoded by a nucleic acid of aspect one or aspect two, or part thereof, or a protein comprising said polypeptide in the preparation or manufacture of a medicament for the treatment of a skin cancer or disorders associated with melanoma and/or disorders of pigmentation, and/or abnormal function, localisation or growth of melanocytes. In another aspect, there is provided a method of diagnosing and/or treating a skin cancer comprising the step of administering to a subject in need of said treatment an effective amount of an inhibitory or interfering RNA or DNA sense or antisense sequence capable of blocking or inhibiting expression of a nucleic acid molecule of aspect one or aspect two, or part thereof, or an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or part thereof, or a protein comprising said peptide or polypeptide, or a protein having SEQ. ID No.3.
Preferably, the skin cancer is melanoma. In another aspect, there is provided a method of screening for the presence of a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, in a sample, comprising: a) contacting a biological sample with a nucleic acid having a sequence that is complementary to nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof; and b) determining whether the nucleic acid binds to a nucleic acid molecule in the sample.
In another aspect, there is provided a method of screening for the presence of a peptide or polypeptide or part thereof, encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, in a sample, comprising: a) contacting a biological sample with an antibody that specifically binds to the peptide or polypeptide, or part thereof; and b) determining whether the antibody binds to the peptide or polypeptide, or part thereof, in the sample.
In another aspect, there is provided a method of screening for the presence of a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, and at least one other nucleic acid molecule which codes for a cell marker commonly used to identify cells of melanocyte lineage in a sample, comprising: a) contacting a biological sample with i) a nucleic acid molecule having a sequence that is complementary to nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof, and ii) a nucleic acid molecule having a sequence that is complementary to the at least one other nucleic acid molecule or part thereof; and b) determining whether the nucleic acid molecules bind to the nucleic acid molecules in the sample. In another aspect, there is provided a method of screening for the presence of a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, and at least one other polypeptide which is a cell marker commonly used to identify cells of melanocyte lineage in a sample, comprising: a) contacting a biological sample with i) an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, and ii) an antibody that specifically binds to the at least one other polypeptide; and b) determining whether the antibodies bind to their corresponding polypeptides in the sample. The cell marker commonly used to identify cells of melanocyte lineage may be selected from for example, melanA, gplOO, tyrosinase, trp-1 and trp-2. It will be understood however, that any other markers that identify melanocyte cell origin can also be used in conjunction with the present invention.
The use of the cell marker encoded by any one of SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8 in a panel of other markers is advantageous since not all cancerous cells express traditional markers such as gplOO or melanA, and the like, which are typically used in methods for screening for melanoma. Inclusion of an additional marker such as that of the present invention significantly enhances the diagnostic power of the diagnostic methods used.
In another aspect, there is provided a method of diagnosing and/or detecting skin cancer or skin condition comprising: a) contacting a biological sample with a nucleic acid having a complementary sequence to nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof; and b) detecting localisation of the nucleic acid as an indicator of the presence (and/or type) of skin cancer or skin condition.
In yet another aspect, there is provided a method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof; and b) detecting localisation of the antibody as an indicator of the presence (and/or type) of skin cancer or skin condition. In another aspect, there is provided a method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with a nucleic acid having a complementary sequence to nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof, and one or more other nucleic acids complementary to nucleic acid molecules selected from the group comprising, but not limited to melanA, gplOO, tyrosinase, trp-1 and trp-2, or parts thereof; and b) determining localisation of the nucleic acids as an indicator of the presence (and/or type) of skin cancer or skin condition. In yet another aspect, there is provided a method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, and at least one other antibody that binds to a polypeptide encoded by melanA, gplOO, tyrosinase, trp-1 and trp-2, or parts thereof, and b) determining localisation of the antibodies as an indicator of the presence (and/or type) of skin cancer or skin condition.
In another aspect, there is provided a method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with a panel of nucleic acid molecules or parts thereof, comprising melanA, gplOO, tyrosinase, trp-1 and trp-2 and a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof; and b) determining localisation of the nucleic acid molecules as an indicator of the presence (and/or type) of skin cancer or skin condition.
In yet another aspect, there is provided a method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with a panel of antibodies that bind specifically to melanA, gplOO, tyrosinase, trp-1 and trp-2 and a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof; and b) determining localisation of the antibodies as indicator of the presence (and/or type) of skin cancer or skin condition.
Preferably, the biological sample used in the method of diagnosing skin cancer is selected from the group consisting of a tissue biopsy, a biological fluid and a surgical specimen. It will be understood, however, that the diagnosis and/or detection of skin cancer with nucleic acid molecules and antibodies of the present invention may also be conducted in vivo or ex vivo. Preferably, the nucleic acid molecules or antibodies used in the method of screening or diagnosis are tagged with a visible or detectable marker to permit visual inspection or measurement/detection. The tag is preferably selected from a group consisting of a fluorescent dye, an isotope, an enzyme (e.g. peroxidase or alkaline phosphatase), a chemical moiety (e.g. biotin) that binds another labelled ligand (e.g. avidin) with high affinity.
Preferably, the skin cancer to be screened, diagnosed or treated is melanoma. Additionally the melanoma can be in the form of a cutaneous melanoma, a melanoma of the nail bed, a melanoma of the eye or a mucosal melanoma. Alternatively, the skin cancer to be screened, diagnosed or treated may be of metastatic origin.
The skin condition may be a disorder of pigmentation, and/or abnormal function, localisation or growth of melanocytes.
In another aspect, there is provided a method of modulating expression of genes associated with skin cancer or skin condition comprising contacting a cell with a short interfering nucleic acid molecule directed against a nucleic acid sequence selected from
SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ.
ID. No. 7, and SEQ. ID. No. 8, or part thereof.
Preferably, the short interfering nucleic acid molecule is selected from a group consisting of short interfering RNA (siRNA), double stranded RNA, micro RNA and short hairpin DNA.
In another aspect, there is provided a method of modulating expression of genes associated with skin cancer or skin condition comprising contacting the cells with an antisense nucleic acid molecule directed against a nucleic acid sequence selected from
SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof.
Preferably, the skin cancer is melanoma.
In another aspect there is provided the use of a nucleic acid molecule comprising a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, or an inhibitory or interfering RNA or DNA sense or antisense sequence, or an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of aspect one or aspect two, or a part or variant thereof, or a protein comprising said peptide or polypeptide, in the treatment of disorders associated with melanoma and/or disorders of pigmentation, and/or abnormal function, localisation or growth of melanocytes.
Preferably the disorders of pigmentation, whether or not in association with melanoma or other skin cancer, include hyperpigmentation disorders such as melasma, cafe au lait macules, drug-induced hyper-pigmentation and phototoxic reactions or hypo- pigmentation disorders such as vitiligo. Further, blockade of immune recognition of a peptide encoded by SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof, or a protein comprising said peptide, can also be used to treat skin disorders caused by immune attack on melanocytes, for example autoimmune vitiligo (Ogg GS, Dunbar PR, Romero P, Chen JL, Cerundolo V (1998) High frequency of skin-homing melanocyte-specific cytotoxic T lymphocytes in autoimmune vitiligo. Journal of Experimental Medicine 188:1203-8). More preferably, the disorders of pigmentation is selected from hypo- pigmentation and/or hyper-pigmentation. In another aspect, there is provided a method of modulating expression of genes associated with changes in skin pigmentation or cosmetic lightening or darkening of skin tone, comprising contacting a cell with an inhibitory or interfering RNA or DNA, sense or antisense, sequence directed against a nucleic acid molecule of aspect one or aspect two. The nucleic acid molecules and antibodies of present invention may be formulated into pharmaceutical preparations by any number of processes well known in the art and may include injectable, topical, oral, slow release and other suitable dosage forms and preparations.
The present invention is suitable for the diagnosis and/or treatment of skin cancers, in particular melanoma.
In the context of the present invention the term "LOCI 46481" is used for convenience to describe the genomic locus LOC 146481. Novel nucleic acid sequences of the present invention in addition to being allocated SEQ ID Nos. may also be referred to as "SHML" sequences (Specific for Human Melanocyte Lineage). It will be understood that the acronym is merely a convenient designation and should not be construed to limit the nucleic acid or the protein to human origin only. The present invention encompasses both mammalian and non-mammalian species SHML. The terms "SHML mRNA", "SHML gene", "SHML transcript" and "SHML protein" may be used interchangeably with specific SEQ ID nos. and are intended to describe the nucleic acid, mRNA and protein sequences of the present invention.
The terms "nucleotide", "nucleic acid", "polynucleotide", "nucleic acid sequence" and the like, as used in the context of the present invention, are intended to encompass a gene, DNA, ssDNA, cDNA, synthetic DNA, RNA, genomic sequences and derivatives thereof.
The terms "peptide" and "polypeptide" as used in the context of the present invention are intended to encompass peptides and fragments of polypeptides or proteins which comprise an amino acid sequence encoded by SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or parts thereof. Such sequences may be detectable by an antibody raised against a peptide encoded by SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof, such as for example SEQ ID No. 3 or part thereof. The term "treatment" as used herein covers any treatment of a disease and/or condition in an animal, particularly a human, and includes:
(i) preventing a disease and/or condition from occurring in a subject which may be predisposed to the disease and/or condition but has not yet been diagnosed as having it; (ii) inhibiting the disease and/or condition, i.e., arresting its development; or (iii) relieving the disease and/or condition, Le., causing regression of the disease and/or condition.
Reference to an "antibody" or "antibodies" includes reference to all the various forms of antibodies, including but not limited to: full antibodies (e.g. having an intact Fc region), including, for example, monoclonal antibodies; antigen-binding antibody fragments, including, for example, Fv, Fab, Fab' and F(ab')2 fragments; humanized antibodies; human antibodies (e.g., produced in transgenic animals or through phage display); single domain antibodies and immunoglobulin-derived polypeptides produced through genetic engineering techniques. Unless otherwise specified, the terms "antibody" or "antibodies" and as used herein encompasses both full antibodies and antigen-binding fragments thereof.
It is anticipated that the treatments described herein can be administered by oral or parenteral routes, including intravenous, intramuscular, intraperitoneal, subcutaneous, rectal and topical administration, and inhalation. For oral administration, the treatments will generally be provided in the form of tablets or capsules or as an aqueous solution or suspension.
Tablets for oral use may include the active ingredient mixed with pharmaceutically acceptable excipients such as inert diluents, disintegrating agents, binding agents, lubricating agents, sweetening agents, flavouring agents, colouring agents and preservatives.
For intramuscular, intraperitoneal, subcutaneous and intravenous use, the treatments will generally be provided in sterile aqueous solutions or suspensions, buffered to an appropriate pH and isotonicity. As used herein, "pharmaceutically acceptable carrier" includes any material which, when combined with an active ingredient, allows the ingredient to retain biological activity and is non-reactive with the subject's immune system. Examples include, but are not limited to, any of the standard pharmaceutical carriers such as a phosphate buffered saline solution, water, emulsions such as oil/water emulsion, and various types of wetting agents. Preferred diluents for aerosol or parenteral administration are phosphate buffered saline or normal (0. 9%) saline.
For methods of preparing various types of formulations and choice of carriers, excipients and additives, see standard pharmacy texts and manuals, such as for example, Remington: The Science and Practice of Pharmacy, 19th Ed., Mack Publishing Co., 1995, the Theory and Practice of Industrial Pharmacy, Lachman L., et al. Lea & Febiger, Philadelphia 3rd Edition, Bentley's Textbook of Pharmaceutics Ed. EA Rawlings Ballilliere Tindall, London 8th Edition, incorporated in its entirety herein by reference.
Unless the context clearly requires otherwise, throughout the description and the claims, the words "comprise", "comprising", and the like are to be construed in an inclusive sense as opposed to an exclusive or exhaustive sense; that is to say, in the sense of "including, but not limited to".
BRIEF DESCRIPTION OF THE FIGURES
Figure 1: The PCR products derived from human melanocyte cDNA encoding SHML Sequence 1. AU sequences are shown 5'- 3'. A) PCR product 1 - SEQ ID No. 9 - shows 486bp of the sequence of the PCR product generated from human melanocyte cDNA with forward primer 12F (5'- TGAGCCAGGAGCTCCACCAT-3') and reverse primer 1145R (5'- GC ACCC AGCTCAAGCCTC AT-3 ; B) PCR product 2 - SEQ ID No. 10 - shows 546bp of the sequence of the PCR product generated from human melanocyte cDNA with forward primer 527F (5'- TGGTCAGGATGGAGGGGAAG-3') and reverse primer 1145R (5'- GCACCCAGCTCAAGCCTCAT-3 '); C) Alignment of two PCR products in A) and B), which overlap by lObp, to make
SEQ. ID. No. 1. The protein-encoding open reading frame (ORF) is underlined - this is SEQ. ID. No. 2.
D) SEQ. ID. No.2 - ORF encoding protein
E) SEQ. ID. No. 3 is the protein sequence encoded by the underlined portion of SEQ. ID. No. 2.
Figure 2: Excerpt of the GenBank entry for the human FRG2 gene sequence Figure 3: Alignment of SHML protein sequence (SEQ. ID. No. 3) with FRG2 protein sequence (by Needleman-Wunsch global alignment, Geneious software, www.geneious.com). Potential nuclear localisation signals are boxed, and a potential protein kinase C phosphoryation site is underlined.
Figure 4: Expression of SHML, tyrosinase & melanA relative to the house-keeping gene HPRT in cDNA from human tissues, cell lines, and primary cell cultures. Expression of these three genes was quantified with quantitative RT-PCR relative to the housekeeping gene HPRT, which was expressed in all samples. SHML expression was detected in human skin, which contain melanocytes, and also in cultured human melanocytes, but not cultured human dermal fiboblasts. The melanocyte-associated gene tyrosinase and melanA were also expressed in human skin and melanocytes, but not dermal fibroblasts. A screen of these genes' expression in cDNA derived from 18 normal adult human tissues (Clontech), revealed 15 of these tissues did not express any of these genes. However, normal brain, spinal cord, and testes expressed all three genes. We conclude that expression of SHML in normal tissues is restricted to melanocytes, and to normal adult tissues that contain cells of melanocytic lineage, namely skin, neural tissue, and testes. Similar experiments carried out in human lymph node samples infiltrated with metastatic melanoma revealed one ("MH") of four samples that expressed tyrosinae and melanA also expressed SHML, confirming that SHML is expressed in some human melanoma samples freshly isolated from patients. None of the three genes were expressed in a single sample of human lymph node that was not infiltrated with melanoma cells. When similar experiments were conducted on six human melanoma cell lines, SHML was expressed in four of the six, including one (MZ2) which did not express either tyrosinase or melanA. Data shown are the average of triplicate measurements, with error bars representing the standard error of the mean. Figure 5: siRNA knockdown in melanoma cell lines DAGI The melanoma cell line DAGI that expresses SHML and tyrosinase was treated with siRNAs targeting SHML and tyrosinase mRNA. Expression of SHML and tyrosinase were then measured by quantitative RT-PCR, and cells treated with siRNAs were compared with untreated cells. 1OnM siRNA targeting SHML mRNA achieved approximately 70% knockdown of SHML expression, similar to the level of knockdown seen with previously- validated siRNAs targeting tyrosinase mRNA. 5OnM siRNA had similar effects, but InM siRNAs were less effective. These data indicate the siRNAs used were capable of significantly knocking down SHML mRNA expression at both the 1OnM and 5OnM doses. Data shown are the average of triplicate measurements, with error bars representing the standard error of the mean. Figure 6: siRNAs targeting SHML gene expression
The two siRNA sequences used to knock down SHML expression in Figure 6 are shown, along with the positions of the sequences they target in the SHML sequence (bold and underlined in SEQ. ID. No. 1 as shown) Figure 7: Alternate transcripts coding for SHML. A)-D) Four predicted alternate transcripts are shown that are capable of encoding SHML protein (SEQ. ID. No. 3), each full length from transcription initiation site (TCATTCTT, nucleotides 1-8 in each transcript) to poly- A tail start. The coding sequence is underlined in each sequence. Three polymorphic sites are highlighted in each sequence by use of a bold capitalised A or G. The first site is an A/C polymorphism at residue 376 (SNP_ID=3751731), although all transcripts observed to date have an A at this position. The second site is a G/A polymorphism at residue 416 (SNP_ID=238004), and although this is encoded as A in the human genome reference sequence, all transcripts observed to date have a G at this position, as shown. The third site is a G/T polymorphism (SNP_ID=11541272), and all transcripts to date have a G at this site, as in the human genome reference sequence (the precise position in each transcript changes due to alternate splicing upstream). E) Alignment of the 4 alternate transcripts to show the region of alternative splicing. The first 360bp of each sequence, and the sequences 3' to the regions shown here, have been omitted, since they are identical between the transcripts. Figure 8: Features of the SHML promoter region.
4192bp of genomic DNA (- strand) is shown immediately 5' to, and including, the SHML transcription start site at the beginning of the transcripts in Figure 8 (SEQ. ID. Nos. 4-7). Important features are shown according to the key below, using combinations of bold, upper case, and underlined text.
115..122 cAMP Response Element (TTATGTAA) (BOLD, UPPER CASE) 477..484 cAMP Response Element (TGAGGTTA) (BOLD, UPPER CASE)
707..711 Putative CCAAT box (underlined only)
1231. .1235 Putative CCAAT box (underlined only)
1487. .1491 Putative CCAAT box (underlined only)
1957. .1961 Putative CCAAT box (underlined only)
3136. .3140 Putative CCAAT box (underlined only)
338..344 Putative TATA box (bold only) 1418..1424 Putative TATA box (bold only) 1729..1735 Putative TATA box (bold only) 3443..3449 Putative TATA box (bold only) 3474..3480 Putative TATA box (bold only) 3779..3785 Putative TATA box (bold only) 3904..3910 Putative TATA box (bold only) 3943..3949 Putative TATA box (bold only) 541..546 Putative Mitf binding site (CACATG) (UPPER CASE,
UNDERLINED)
843. .848 Putative Mitf binding site (CATGTG) (UPPER CASE,
UNDERLINED)
1657 ..1662 Putative Mitf binding site (CATGTG) (UPPER CASE,
UNDERLINED)
2067 ..2072 Putative Mitf binding site (CACATG) (UPPER CASE,
UNDERLINED)
3352 ..3357 Putative Mitf binding site (CATGTG) (UPPER CASE,
UNDERLINED)
3578 ..3583 Putative Mitf binding site (CACATG) (UPPER CASE,
UNDERLINED)
3209..3218 CpG island, a potential transcription initiation site and SPl Transcription Factor binding site (UPPER
CASE ONLΪ) 4185..4192 Transcription Start Site (TCATTCTT) (bold, underlined)
4018 Site of a Single-Nucleotide Polymorphism (C/T, SNP #11647911)
(BOLD, UPPER CASE, UNDERLINED)
DESCRIPTION OF THE PREFERRED EMBODIMENT
The present invention is based on a surprising observation that an uncharacterised gene in the human genome encodes a protein that is present in cells of melanocy e lineage, but not other cells. For convenience the novel nucleic acid sequence that encodes the novel, cell-specific protein, provided herein is designated
"SHML".
Discovery of the protein encoded by the SHML gene Based on bioinformatic analysis of Expressed Sequence Tags and mRNA sequences in public databases, it was predicted that mRNA encoded from a genomic locus LOC146481 might be expressed exclusively by cells of melanocytic lineage. The mRNA obtained from human melanocytes was sequenced (SEQ. ID. No. I5 see also Figure 1) and showed that it was expressed by human melanocytes. SEQ. ID. No. 1
ATATGTCTCAATGGTGGATGTAGGGAAACTTCACAGGCTTTGATGGGACTGAGG TGGTGTCTGTTGTGTGAAGACAGGAGCTGAATGCTCAGGATCTAGGCTGCTTTT CTTGTGGTCAGTTGGGTTACCTGTTTGGGACCAAGTCCATGTTTACTAAGGAGG CTGAATAAATTCTACAGAGGAAAGTGGAGCTCCCAGGATGACCGAGGAAGGGTA AGAAAAGGGAACCAGAGTCGAGCTCACATGAGGGAAACTCCAAGAAAAGGAAAA TCGGTTCCAAGGACAGCTGCCAAGACAGAGCTGGTAGAATTTTGCCTTTTTCCC CCAAAGGGAAAATAAGCAGTTGACTTTTATAGAGGGTTTGAGCAGCAAGGTGAC TGAAAAAATTTTTGAGATCCTGGCACTCAGAGAATATTTGGGGACTCAGAAGGT GTTAAATTTCACTTCATTTAAGTACTAATATGGTCAGGATGGAGGGGAAGATTC AAATGTTCACCTGAAGGTGCATGGGAGGTTTTGGAAATGAGGGTCGGTGGGAAC TGTGCTGGCGAGTATCTCACTCACATGCTTCTTTTGCGGGGATCTGTCCAGGAG AGGAGCACAGCTTGATGTTGAAAAAGAAACTAAAGTCCTCCACTTTGCACAGCA ATAAACTCAAGGAGACCTGTGATGCCCACCACAGAGGGCCTTTCATGACTCACA CTGGGTGCACCAAGCAGCACAGGTCTCAGACCCTAGGAGTTCAATGGCTGTCAT TTCAGAAAAGCTTGGTGACTTTACAAGCTGTGTCAAGGCCATTTATCAAGACCT ATACTGGGTATCGGTGCAGCAGGTCCATTCTCCACTGACCTGGGAGCAGCTCAC TCAGCTTGCCCGGTTCTGGCGGCCTCTATGTGCTCAGGTGCAGACCTTCTATTT TATAGCCACCCAGGTAGGTTATGTCTTCCCTGCTAAGAACTGGCTTGTTTCAGC CACATTGCCTGGCCCTGGGGATCCAGCCCTGGATAGAGAAGCCCATCCCT
The protein-encoding open reading frame (ORF) from SEQ. ID. No. 1 mRNA is the nucleotide sequence shown below (SEQ. ID. No. 2): SEQ. ID. No. 2
ATGGGAGGTTTTGGAAATGAGGGTCGGTGGGAACTGTGCTGGCGAGTATCTCAC TCACATGCTTCTTTTGCGGGGATCTGTCCAGGAGAGGAGCACAGCTTGATGTTG
AAAAAGAAACTAAAGTCCTCCACTTTGCACAGCAATAAACTCAAGGAGACCTGT
GATGCCCACCACAGAGGGCCTTTCATGACTCACACTGGGTGCACCAAGCAGCAC
AGGTCTCAGACCCTAGGAGTTCAATGGCTGTCATTTCAGAAAAGCTTGGTGACT
TTACAAGCTGTGTCAAGGCCATTTATCAAGACCTATACTGGGTATCGGTGCAGC AGGTCCATTCTCCACTGA
This ORF is one of several possible ORFs in SEQ. ID. No. 1, but based on the present findings of the encoded protein's high homology to another human protein, as described below, SEQ. ID. No. 2 was identified as the protein coding sequence. The protein encoded by SEQ. ID. No. 2 has the following amino acid sequence (SEQ. ID. No. 3):
SEQ. ID. No. 3
MGGFGNEGRWELCWRVSHSHASF AGICPGEEHSLMLKKKLKSSTLHSN KLKETCDAHHRGPFMTHTGCTKQHRSQTLGVQWLSFQKSLVTLQAVSR PFIKTYTGYRCSRSILH Sequence comparison of SEO. ID. No. 3 with FRG2 and other sequences from LOC146481
SEQ. ID. No. 3 has significant homology to another known protein, called FRG2 (FSHD region gene 2), the sequence of which is given in Figure 2, along with other information on the gene encoding FRG2 protein. FRG2 is a gene implicated in facioscapulohumeral muscular dystrophy (T. Rijkers et al, FRG2, an FSHD candidate gene, is transcriptionally up-regulated in differentiating primary myoblast cultures of FSHD patients. J. MedGenet. 2004;41; 826-836). Alignment of the SEQ. ID. No. 3 with FRG2 protein sequence is shown in Figure 3. In this alignment, 50 of 113 amino acids in SEQ. ID. No. 3 protein are identical to those in FRG2, for 44% overall homology. The most remarkable features of this alignment are that amino acids 24 and 90 of SEQ. ID. No. 3 protein align with FRG2 amino acids 110-177 with only a single gap. Across this 67 amino acid sequence of SEQ. ID. No. 3 protein, there is identity with FRG2 amino acids at 39 sites (58% homology), with complete homology over a 9 amino acid sequence at sites 52-60 in SEQ. ID. No. 3 and sites 139-147 of FRG2. These proteins are therefore highly likely to be related. The protein sequence of FRG2 is annotated as having two sequences that confer nuclear localisation, at amino acids 96-99 (sequence RKRK) and 157-160 (sequence KRHR). The SEQ. ID. No. 3 has a homologous protein sequence for only the second sequence at amino acids 70-73 (sequence KQHR). SEQ. ID. No. 3 does have a potential nuclear localisation signal (sequence LKKKLKS) that is not present in FRG2 (using PredictNLS online http://cubic.bioc.columbia.edu/cgi/var/nair/resonline.pl). Based on these findings it is therefore likely that the SEQ. ID. No. 3 protein will localise to the nucleus of the cell after translation, as does FRG2.
The sequence SNKL at amino acids 47-50 in the SEQ. ID. No. 3 protein is a potential protein kinase C (PKC) phosphorylation site, implicating PKC as a regulator of the protein's function. The SEQ. ID. No. 3 protein is thus potentially capable of post- translational modification by phosphorylation at this site.
As a precedent, there are other nuclear factors involved in melanocyte differentiation such as MITF (microophthalmia-associated transcription factor) and CREB (cAMP-responsive element binding protein) that are regulated by phosphorylation.
Sequence comparison of SEQ. ID. No. 1 and SEQ. ID. No. 3 with other sequences from LOC146481
The genomic locus LOC146481 had been predicted by NCBI to encode mRNAs (XR_017714.1, XR_017753.1, and XR_041323.1), different from that identified herein as SEQ. ID. No. 1. These predicted mRNAs (XR_017714.1, XRJH7753.1, and XR_041323.1), had been predicted to encode a protein different from SEQ. ID. No. 3 described herein (predicted hypothetical protein XPJ)01723191.1). One mRNA sequence previously filed in GenBank (National Institutes of Health Mammalian Gene Collection project (NIH MGC) also differs from SEQ. ID. No. 1, and has several reading frames. No protein sequence had ever been predicted from this single mRNA sequence, primarily because: a lack of any data regarding its potential function; doubts about its veracity given it was only partially homologous to the predicted mRNAs XR_017714.1, XR_017753.1, and XR_041323.1; and uncertainty about which of several potential open-reading frames within BC023607 encoded protein.
In analysing SEQ. ID. No. 1 of the present invention, it was found that one of several open-reading frames encoded a protein with strong homology to another human protein, FRG2. Based on analytical and comparative studies described above, particularly the recognition that the sequence was restricted to cells of the melanocytic lineage and, on the basis of strong homology to another protein, (that only one of the open-reading frames present in SEQ. ID. No. 1 was likely to encode protein) the present invention provides a novel nucleotide sequence, SEQ. ID. No.l, the mRNA sequence included therein, SEQ. ID. No. 2, and the corresponding protein sequence, SEQ. ID. No. 3. The restriction of the sequences to cells of the melanocytic lineage, indicates a function related to the specialised properties of such cells, as described below. Expression of SHML transcripts in human tissues and cells
Gene expression analysis by quantitative RT-PCR conducted on cDNA from normal human tissues showed that expression of "SHML" gene was restricted to tissues containing cells of melanocytic lineage, namely skin and neural tissue (Fig 4). Similar analysis on normal cell lines showed that SHML is expressed by cultured melanocytes, but by neither keratinocytes nor fibroblasts (Fig 4). These results identify the SHML as expressed specifically in cells of melanocytic lineage. A majority of melanoma cell lines were also found to express SHML (Fig 4). One well- characterised melanoma cell line MZ2 expresses SEQ ID No. 1 but not the nucleic acid encoding melanA, gplOO or tyrosinase, which are commonly used to identify cells as being of melanocyte lineage. This single experiment confirms the utility of SEQ ID No.l, the mRNA sequence, SEQ ID No. 2, and the corresponding protein sequence, SEQ ID No. 3, as markers in cancer diagnosis (Fig 4).
The gene and its corresponding protein will therefore have value as a diagnostic marker for confirmation of diagnosis of cancers such as melanoma, a marker of a melanocyte cell lineage, as a therapeutic drug target, for example as a target for immunotherapy of melanoma or a drug target for melanoma or disorders of pigmentation. Its corresponding antibody will also have value as a diagnostic tool or as a treatment/therapy for melanoma in its various forms and for disorders associated with melanoma and/or disorders of pigmentation. Functional roles of SHML protein
To investigate the function of the SHML protein, the SHML mRNA was knocked down using siRNA, as shown in Fig 5. A melanoma cell line (DAGI) was exposed to siRNAs targeting SHML mRNA (both siRNAs shown in Fig 6), as well as control siRNAs targeting the melanocyte marker tyrosinase. Subsequent quantitative RT-PCR analysis confirmed knockdown of SHML mRNA by at least 60% even at 1OnM concentrations of siRNAs (Fig 5). This was equivalent to the knock down in tyrosinase mRNA concentrations in the same experiment, carried out with siRNAs that had been previously validated. DAGI cells with and without SHML mRNA knockdown were subjected to whole genome microarray analysis, to detect gene modulated by SHML.
Without wishing to be bound by theory or any particular mechanism of action, analysis of SHML siRNA knockdown using human whole genome microarrays, revealed that DKKl transcription is regulated by SHML. This finding was subsequently confirmed using quantitative RT-PCR (data not shown). DKKl is a secreted protein involved in regulation of the Wnt signalling pathway.
Wnt proteins interact with a cell surface receptor complex consisting of Frizzled and LRP5/6, resulting in stabilisation of cytoplasmic β-catenin. β-catenin accumulates in the cytoplasm and moves to the nucleus. Once in the nucleus β-catenin interacts with the LEF/TCF family of transcription factors to activate transcription of TCF/LEF target genes. DKKl is able to inhibit Wnt signalling at the cell surface by binding to LRP5/6 component of the Wnt receptor complex. The complex is endocytosed upon DKKl binding, thereby blocking the ability of Frizzled to send the Wnt signal upon binding of Wnt. (1)
In melanocytes Wnt signalling is crucial in development, differentiation, and pigmentation. Wnt signalling is required to maintain melanocyte precursor cells in a stem cell like state during development. Wnt signalling has been shown to control pigmentation by activation of Mitf-M transcription via the TCF/LEF1 binding site in the Mitf-M promoter. Wnt signalling in melanocytes results in the β-catenin/TCF/LEF complex increasing transcription of Mitf-M. Downstream of Mitf-M the pigmentation pathway is activated and melanosomes are produced. (2-4)
SHML protein therefore appears to be a negative regulator of DKKl expression. Reduction in SHML mRNA levels resulted in increased DKKl mRNA expression levels, as demonstrated herein. SHML protein is a putative transcription factor and may regulate DKKl mRNA levels via interaction with the DKKl promoter. Thus, SHML protein is a melanocyte-specific regulator of the Wnt signalling pathway, which has been shown to be required for melanocyte development, differentiation and pigmentation. The tissue specificity of SHML protein expression enables systemic drug treatment with a tissue specific effect on Wnt signalling.
Successful inhibition of SHML gene expression with siRNA
As shown in Fig 56, siRNAs were used to successfully knock down expression of SHML mRNA in melanoma cells by at least 60%, with subsequent effects on the transcription of other genes, notably DKKl. The location of the sequences successfully targeted by siRNAs are shown in Fig 6, along with the siRNA sequences. These sequences are located at residues 552-570, and 637-655 of the SEQ. ID. No. I5 and were targeted by siRNAs 293438 and 293439 (provided by Applied Biosystems/Ambion, Austin, TX, USA). The siRNAs have similar efficacy when used individually as when combined. These experiments demonstrated that expression of SHML mRNA could be successfully knocked down using an RNA inhibition approach, with subsequent effects on the expression of other genes. Alternate transcripts from SHML
Analysis of genomic data available from public databases (including human genome sequences and expressed sequences, including Expressed Sequence Tags and other mRNAs) allows the full length sequences of possible alternate transcripts from SHML to be deduced. Most of these alternate transcripts encode the protein SEQ. ID. No. 3, and these transcripts are shown in Fig 7, including the full length mRNA that incorporates SEQ. ID. No. 1 (labelled "transcript 1", SEQ. ID. No. 4). As shown in Fig 8, the transcripts differ in their inclusion of a 12bp sequence at the end of the first exon, and the inclusion of an additional lOObp exon before the coding sequence. Experimental evidence shows transcripts including the lOObp additional sequence shown in transcripts 2 and 4 (SEQ. ID. No. 5 and SEQ. ID. No. 7) because RT-PCR of cDNA from cells of melanocytic origin using primers that span this region of cDNA occasionally produce two bands that differ in size by lOObp (data not shown).
There are also Single Nucleotide Polymorphisms (SNPs) in the genomic DNA that encodes these transcripts. Therefore allelic variants of all 4 alternate transcripts are possible, though none of these affect the encoded protein, because they are located in the untranslated regions of each mRNA. The positions of the 3 possible polymorphic residues in each transcript are noted in Fig 7 with bolded, capitalised letters. All 4 alternate transcripts have a possible AJC polymorphism at residue 376 (SNP_ID=3751731). All 4 alternate transcripts also have a possible G/A polymorphism at residue 416 (SNP_ID=238004). A G/T polymorphism (SNPJD=I 1541272) exists at the other site in bold capitals in each transcript (the precise location changes due to the alternate splicing upstream). It is therefore possible that any of the 4 alternate transcripts may carry any one of the 3 nucleotide changes designated at these SNP sites, so up to 32 different mRNA sequences are possible that may all encode the protein sequence SEQ. ID. No. 3 in different individuals. Only the 4 most likely alternative transcripts are shown in Fig 7, although all variants due to SNPs, as described above are included in the scope of the present invention. Promoter analysis
Analysis of over 4kb upstream of the transcription initiation site (the beginning of the transcripts shown in Fig 7) revealed clusters of numerous sequences that are likely to be involved in regulating gene expression, especially by binding transcription factors and regulatory proteins. As shown in Fig 8, these regulatory elements include eight TATA boxes, five CCAAT boxes, and one SPl binding sites, likely to be involved in binding general transcription factors and related proteins. There are 6 putative binding sites for MITF (microophthalmia-associated transcription factor) indicating this crucial transcription factor for melanocyte differentiation is involved in regulating "SHML" expression. There are also two cAMP-response elements (CREs) implicating cAMP signalling in the regulation of SHML transcription.
A SNP in this promoter region that might conceivably affect transcription or transcript stability, SNP # 11647911, is a C/T polymorphism transcript start site, as shown at position 4018. This is not predicted to be a site involved in transcription factor binding or transcription initiation, but it is still possible that it will affect the transcription of the gene in different individuals, potentially affecting melanocyte structure or function.
The novel SHML protein described herein, or parts thereof, represents a new and useful target for diagnosis and treatment of skin and other conditions that are caused or mediated by abnormal melanocyte function, growth, proliferation and/or localisation.
The active agents described herein, including anti-sense and sense nucleic acid approaches, and antibodies, to manipulating expression of the SHML protein can be applied to both diagnostic and therapeutic uses in the treatment of melanocyte-mediated disorders, the most important of which is skin cancer such as melanoma. However, cosmetic applications are also contemplated such as alteration of skin and hair pigmentation, masking or removal of skin blemishes and the like. Manipulation of regulatory processes within melanocytes has been clearly demonstrated herein using siRNAs that modulate expression of SHML. The structure of the gene and its regulatory regions, and the protein sequence, provided herein enable other known therapeutic and diagnostic approaches to be adopted for manipulating the expression and/or function of
SHML and hence melanocytes and melanocyte-mediated disorders.
A preferred embodiment of the invention will now be described in more detail by reference to the following non-limiting examples.
EXAMPLES EXAMPLE 1 : General Methods
General laboratory procedures not specifically described herein can be found in the general molecular biology or immunology texts including, for example, Sambrook et al. (1989) Molecular Cloning: A laboratory Manual, Cold Spring Harbor Laboratory: Co Id Spring Harbor, NY, and Harlow et al. (1988) Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory: Co Id Spring Harbor, NY. (i) Melanocyte Cell Culture
Seed Cascade melanocytes (catalogue # C-024-5C, Cascade Biologies Inc. 1341 SW Custer Drive, Portland OR 97219, USA, ph 503 292 9521) at a density of 5x103 cells/cm2 in a 25 cm2 flask with Cascade medium 254 (cat # M254-500) with PMA free melanocyte supplement (cat # S-015-5C).
Thaw vial of 0.5 million cells in a 37°C water bath. Open vial in a laminar flow hood and resuspend cell pellet using a ImL pipette. Remove lOμL and determine cell number using a haemocytometer. Seed cells at density specified above. Incubate at 37°C/5%CO2 for 24 hours then replace the media and remove dead cells. Change media every 2-3 days and passage 1:2 whenever flask becomes confluent. Passage using 2x trypsin.
(ii) DAGI Cell Culture Thaw vial of 0.5 million cells in a 37°C water bath. Open vial in a laminar flow hood and resuspend cell pellet using a ImL pipette. Transfer cells to a 15mL tube then add 1OmL RPMIl 640/10% FBS/lxPSGCpenicillin/streptomycin/glutamate). Mix cells then centrifuge for 5min at 18Og. Remove supernatant, add 5mL RPMI1640/10% FBS/lxPSG, resuspend cells and transfer to a 25 cm2 flask. Incubate at 37°C/5%CO2 for 24 hours then replace the media and remove dead cells. Change media every 2-3 days and passage 1:2 whenever flask becomes confluent. Passage using 2x trypsin.
(iii) Extraction of RNA and cDNA synthesis for microarray and qPCR analysis Materials: Trizol, Invitrogen cat # 15596-026
Mini RNA extraction kit, Qiagen cat # 74104
1st strand cDNA synthesis kit, Invitrogen cat #18080-093
RNA synthesis:
Remove media and add 750μL trizol, using a pipette ensure that cell pellet is fully resuspended. Shear genomic DNA by passing sample through a 21 gauge needle 5 times. Rock the tube at room temperature (RT) for 5 min. Add 150μL chloroform shake vigorously for 15s then incubate at RT for 3min. Spin at 1200Og for 5min at 4°C. Transfer upper aqueous phase to a fresh non-stick RNAse free tube. Add an equal volume of 70% ethanol to the tube and add mix to spin column iη^mL collection tube, centrifuge at 800Og for 15s, discard flow through. Using the Qiagen RNA extraction kit complete the remaining steps following manufacturers instructions. Add 700μL buffer RWl to the column, centrifuge at 800Og for 15s, discard flow through. Add lOμL of DNAse I stock to 70μL buffer RDD, add to column and incubate at RT for 15min. Add 700μL buffer RWl to the column, centrifuge at 800Og for 15s, discard flow through and collection tube.
Transfer column to a clean 2mL collection tube and add 500μL buffer RPE to column, centrifuge at 800Og for 15s, discard flow through. Add 500μL buffer RPE to column, centrifuge at 800Og for 2min, discard flow through & collection tube. Transfer spin column to 1.5mL non-stick RNAse free Eppendorf tube, add minimum 15μL water to centre of the column, centrifuge at 800Og for lmin.
Transfer spin column to 1.5mL non-stick RNAse free Eppendorf tube, add minimum 45 μL water to centre of the column, centrifuge at 800Og for lmin.
Assess quality and quantity of RNA using the nano-drop of both elutes.
Continue only with enough sample for qPCR only, the rest is stored at -8O0C until ready for microarray analysis.
1st strand cDNA synthesis: Use cDNA synthesis kit from Invitrogen and follow manufacturers instructions.
Make same mix for NoRT control, half volume and omit the SSRTIII:
200ng RNA (to 4μL for a lOμL rxn)
0.5μL 50μM oligodT primer
0.5μL 50ng/μL random hexamers 0.5μL 1OmM dNTPs
Incubated @ 65 °C for 5 min then kept on ice for at least 1 min.
Combine following components together before adding to RNAniix: lμL l Ox RT buffer
2μL 25mM MgCl2 lμL O.lM DTT
0.5μL RNAseOUT
0.5μL SSRTIII
Add to RNA mix
Incubated @ 250C for 10 min, then incubated @ 500C for 50 min. Terminate reaction @ 850C for 5 min, then chilled on ice.
Spin to collect reaction, add 0.5μL RNAseH & incubated @ 37°C for 20 min.
Stored @ -200C until used for qRTPCR.
(iv) qPCR for measuring "Target 1" (SHMD siRNA knockdown in DAGI:
Source of nucleic acid: cDNA of siRNA knockdown in DAGI Materials:
Applied Biosystems FAST Taqman PCR mastermix, cat # 4352042
Hypothetical Protein Hs01390151_ml Taqman primer/probe mix, Applied Biosystems cat # 4331182 Methods:
Add 2μL with IOng of sample cDNA all required wells
Add 2μL with corresponding amount to the actual sample for NoRT sample to each required well. ϊ 5 μL of 2x PCR mastermix 0.5μL 2Ox primer/probe mix 2.5μL water
Primer/probe sets
HPRTl
SHML
PCR cycling: 20s @ 950C
40 cycles of — ls @ 95°C
20s @ 60°C
(v) siRNA knockdown of SHML expression in the melanoma cell line DAGI for microarray analysis:
Cell Sources: DAGI
Materials:
Ambion siRNA # 293438, 293439, sequences as shown in Figure 6.
Lipofectamine 2000 ("LF2000"), Invitrogen (USA) cat #11668-027 BlockiT Fluorescent oligo, Invitrogen cat #2013
Methods:
Seed 5x105 cells/well in a 6 well plate with 2mL of RPMI 1640 (Invitrogen) with 10% foetal bovine serum.
Make up LF2000/siRNA mixes - Add 5μL LF2000 per 1 OOμL. Incubate at room temperature for 5min
Add siRNA to lOOμL OM.
Mix siRNA & LF2000 mixes & incubate at room temperature for 20min.
Add siRNA mixes to wells
Change media after 24 hours. Harvested and analyse after 48 hours. AU microarray/qPCR samples were harvested into non-stick RNAse free 1.5mL tubes. Analyse by microarray, qPCR and flow cytometry for BlockiT transfection
Figure imgf000027_0001
(vi) Microarray Information: Chips used - Affymetrix Human Genome Ul 33 Plus 2.0 Array Genechip Users protocol - http://www.affymetrix.com/support/technical/manual/expression_manual.affx Used as protocol for Genechip use from RNA to producing expression data EXAMPLE 2: Determination of tissue expression specificity of the nucleic acid encoding SHML in humans using quantitative real time PCR.
Using Clontech Human Tissue libraries (Clontech Laboratories Inc. 1290 Terra Bella Ave, Mountain View, CA 94043, USA, ph 800.662.2566, catalogue # 636643) SHML mRNA levels were measured by quantitative real time PCR (qPCR) using the Taqman specific assay ID # HsO139O151_ml. Since SHML was suspected to be a melanocyte specific gene, expression of two known melanocyte specific genes, tyrosinase and melanΛ, were also measured using Applied Biosystems Taqman assays, ID # HsOOl 65976_ml & HsOO924233_ml respectively. All qPCR reactions were 45 cycles, triplicates with IOng of each tissue cDNA.
Referring to Figure 5, using the Clontech tissue library, SHML mRNA and the two melanocyte specific genes were all detected in brain, spinal cord & the testes only.
SHML mRNA was also tested in normal human melanocytes (Cascade Biologies), samples of normal human skin and melanoma tumor-infiltrated lymph nodes (TILNs) (obtained from consenting patients), and a number of melanoma cell lines, obtained from collaborating research groups.
Referring to Figure 3, SHML mJRNA was shown to be expressed in skin and at a higher level in normal human melanocytes. SHML mRNA was also expressed in most melanoma cell lines including MZ2 where no other markers of melanocytic origin were expressed.
EXAMPLE 3: Sequencing of the nucleic acid encoding SHML in normal human melanocytes
PCR fragments of the nucleic acid sequence encoding SHML were generated from cDNA synthesized using RNA extracted from normal human melanocytes
(Cascade Biologies catalogue # C-024-5C) using the primers
5'TGGTCAGGATGGAGGGGAAG & 3'-ATGAGGCTTGAGCTGGGTGC.
The resulting PCR product was gel purified using the Qiagen Qiaex II Gel
Extraction kit (Qiagen catalogue # 20021). The PCR product was sequenced using the PCR primers, at 5μM, with approximately 50ng of PCR product per reaction, on a
3130XL capillary sequencer from Applied Biosystems using Bigdye version 3.1 terminator chemistry.
The siRNAs specific for SHML (Ambion siRNA #293438 & # 293439) can be used to knockdown SHML mRNA levels as in the melanoma cell line DAGI. RNA from the siRNA knockdown can be used for microarray experiments. RNA is extracted using the Qiagen Rneasy Mini kit (Qiagen catalogue #74104). Microarray analysis of the RNA generated from these knockdowns can be done using the Affymetrix Ul 33 plus
2.0 human gene expression quantitation arrays. (Affymetrix "Expression Analysis
Technical Manual" Affymetrix, 3420 Central Expressway, Santa Clara, CA 95051, USA. Tel. 408-731-5000. Fax. 408-731-5380.)
Results:
SHML mRNA was found to be expressed in many melanoma cell lines and tumour samples, but was absent from nearly all normal human tissues. Commercial cDNA libraries were sourced from volunteers by the respective companies and information on these donors and tissue processing is available on the company websites; normal human skin and melanoma tumor-infiltrated lymph nodes were sourced from consenting volunteers undergoing plastic surgery and lymph node resection respectively, under appropriate ethics committee oversight, and part of each sample was snap frozen in liquid nitrogen as soon as practicable and stored at -80°C until RNA extraction. However, it was discovered that SHML mRNA was also switched on in skin and some neural samples.
Subsequently, SHML mRNA was found to be expressed in melanocytes, the normal cells that melanoma develops from, and which are found in skin and some neural tissue. Indeed, the expression pattern of SHML mRNA in human cell lines and tissues mirrors other genes that are only switched on in melanocytes. This finding made it highly likely that the gene is specific to cells of the melanocyte lineage, and may even play a role in some of the unique functions of these cells, such as pigmentation. EXAMPLE 4: Expression of SHML protein
The nucleic acid sequence encoding SHML is amplified from a cDNA template using PCR and cloned into expression vectors for protein expression in E. coli, yeast and mammalian cells. The confirmed plasmid is then transfected into the appropriate cell line/cells and expression of the protein can be induced. (Invitrogen Life Technologies Instruction Manual for E.coli Expression System with Gateway Technology, from Invitrogen Life Technologies Ltd, 18-24 Botha Road, Penrose, Auckland 1006, New Zealand.) Recombinant SHML protein is purified from these cellular sources by the use of tags attached to the protein, that are encoded in the expression vector. For expression in mammalian cells the Invitrogen V5 tag system is appropriate for this purpose, since it allows affinity purification using anti-V5 antibodies. (Invitrogen Life Technologies Ltd, 18-24 Botha Road, Penrose, Auckland 1006, New Zealand.) Purified SHML protein is then used as an immunogen for the production of antibodies to SHML EXAMPLE 5: Antigen Synthesis and Conjugation
Production of antibodies is according to standard techniques know, for example those described in Harlow et al. (1988) Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory: Co Id Spring Harbor, NY. Other suitable techniques would be known to those skilled in the art.
Approximately lOmg of peptide is synthesized for the antibody production. The peptide is analyzed by mass spectral and HPLC analyses to ensure sequence integrity and purity prior to conjugation. The peptide is then conjugated to KLH or BSA (2-3mg). The peptide-protein conjugate is purified by gel filtration and freeze dried. The remaining unconjugated peptide is supplied. Immunization and Sera Collection:
Using rabbits as hosts, the conjugated peptide is injected subcutaneously at multiple sites. The initial immunization is given in Complete Freund's Adjuvant with all subsequent immunizations given in Incomplete Freund's Adjuvant. The animals are bled at intervals to ascertain the titer of the antiserum. Antisera are used unpurified. Immunization/Bleed Protocol: A detailed immunization and bleeding schedule is provided below:
Figure imgf000030_0001
Full methods are detailed at: http ://www. sigmaaldrich. com/Brands/S igma_Geno sys/CustomJPeptides/Pro duct__Lines/ Peptide_Antisera. html
Although the invention has been described with reference to certain embodiments and examples it will be understood that variants in keeping with the disclosure and the spirit of the invention are also within its scope.
REFERENCES:
1. Niehrs, C. 2006. Function and biological roles of the Dickkopf family of Wnt modulators. Oncogene 25:7469-7481.
2. Yamaguchi, Y., S. Itami, H. Watabe, K. Yasumoto, Z. A. Abdel-Malek, T. Kubo, F. Rouzaud, A. Tanemura, K. Yoshikawa, and V. J. Hearing. 2004.
Mesenchymal-epithelial interactions in the skin: increased expression of dickkopfl by palmoplantar fibroblasts inhibits melanocyte growth and differentiation. J Cell Biol 165:275-285.
3. Yamaguchi, Y., T. Passeron, T. Hoashi, H. Watabe, F. Rouzaud, K. Yasumoto, T. Hara, C. Tohyama, I. Katayama, T. Miki, and V. J. Hearing. 2008. Dickkopf 1
(DKKl) regulates skin pigmentation and thickness by affecting Wnt/beta-catenin signaling in keratinocytes. Faseb J 22: 1009- 1020.
4. Yamaguchi, Y., T. Passeron, H. Watabe, K. Yasumoto, F. Rouzaud, T. Hoashi, and V. J. Hearing. 2007. The effects of dickkopf 1 on gene expression and Wnt signaling by melanocytes: mechanisms underlying its suppression of melanocyte function and proliferation. J Invest Dermatol 127:1217-1225.

Claims

THE CLAIMS DEFINING THE INVENTION ARE AS FOLLOWS:-
1. An isolated nucleic acid molecule that encodes a melanocyte-specific protein, comprising a nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or functional fragments thereof.
2. The nucleic acid molecule according to claim 1, wherein the nucleic acid molecule encodes a protein having SEQ ID No.3 or a functional fragment thereof.
3. An isolated nucleic acid molecule that encodes a melanocyte-specific protein, wherein the nucleic acid molecule has at least 75% sequence identity with SEQ. ID. No. 1.
4. The nucleic acid molecule according to claim 3, wherein the nucleic acid molecule has from 80% to 95% sequence identity with SEQ. ID. No. 1.
5. A nucleic acid molecule that is complementary to a nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or fragments thereof.
6. A protein comprising a polypeptide sequence encoded by an isolated nucleic acid molecule of any one of claims 1 to 4.
7. A cell marker comprising a peptide or polypeptide sequence encoded by an isolated nucleic acid molecule of any one of claims 1 to 4, or part thereof.
8. A cell marker comprising a peptide or polypeptide sequence comprising SEQ ID No. 3.
9. The cell marker according to claim 7 or claim 8, wherein the cell marker is a skin cell marker.
10. The cell marker according to claim 9, wherein the skin cell is a melanocyte.
11. The cell marker according to any one of claims 7 to 10, wherein the cell marker is a marker for a skin-related neoplastic condition.
12. The cell marker according to claim 11, wherein the neoplastic condition is melanoma.
13. An antibody that binds to the peptide or polypeptide sequence encoded by a nucleic acid molecule of any one of claims 1 to 4, or part thereof, or to a protein comprising SEQ ID No. 3, or part thereof.
14. The antibody according to claim 13, wherein the antibody is a monoclonal antibody or a functional fragment thereof.
15. A pharmaceutical composition comprising an antibody according to claim 13 or claim 14, optionally in combination with a pharmaceutically acceptable carrier.
16. A vector comprising a nucleic acid sequence set forth in any one of claims 1 to 5, or a part thereof, operatively linked to a promoter.
17. A prokaryotic or eukaryotic cell comprising the expression vector according to claim 16.
18. A prokaryotic or eukaryotic cell according to claim 17, wherein the prokaryotic cell is a bacterial cell or a fungal cell.
19. A prokaryotic or eukaryotic cell according to claim 17, wherein the eukaryotic cell is selected from a mammalian cell, an avian cell, an amphibian cell, a reptilian cell or an insect cell.
20. Use of a nucleic acid molecule of any one of claims 1 to 4, a peptide or polypeptide encoded by a nucleic acid molecule of any one of claims 1 to 4, or part thereof, or a protein comprising said peptide or polypeptide, as a marker of a melanocyte cell lineage.
21. Use of a protein having SEQ ID No.3, or part thereof, as a marker of a melanocyte cell lineage.
22. Use of an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of any one of claims 1 to 4, or part thereof, or a protein comprising said peptide or polypeptide, for identifying melanocyte cell lineage.
23. Use of a nucleic acid molecule comprising a nucleic acid molecule of any one of claims 1 to 4, or part thereof, or a peptide or polypeptide encoded by a nucleic acid molecule of any one of claims 1 to 4, or part thereof, or a protein comprising said peptide or polypeptide, or a protein having SEQ ID No.3, or part thereof, or an antibody that specifically binds to said peptide or polypeptide and/or said protein, in the diagnosis and/or detection of a skin cancer.
24. Method of diagnosing and/or treating a skin cancer comprising the step of administering to a subject in need of said treatment an effective amount of an inhibitory or interfering RNA or DNA sense or antisense sequence capable of blocking or inhibiting expression of a nucleic acid molecule of any one of claims
1 to 4, or part thereof, or an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of any one of claims 1 to 4, or part thereof, or a protein comprising said peptide or polypeptide, or a protein having SEQ ID No.3.
25. A method of screening for the presence of a nucleic acid molecule of any one of claims 1 to 4, or a part or variant thereof, in a sample, comprising: a) contacting a biological sample with a nucleic acid having a sequence that is complementary to nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID.
No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof; and b) determining whether the nucleic acid binds to a nucleic acid molecule in the sample.
26. A method of screening for the presence of a peptide or polypeptide or part thereof, encoded by a nucleic acid molecule of any one of claims 1 to 4, or a part or variant thereof, in a sample, comprising: a) contacting a biological sample with an antibody that specifically binds to the peptide or polypeptide, or part thereof; and b) determining whether the antibody binds to the peptide or polypeptide, or part thereof, in the sample.
27. A method of screening for the presence of a nucleic acid molecule of any one of claims 1 to 4, or a part or variant thereof, and at least one other nucleic acid molecule which codes for a cell marker commonly used to identify cells of melanocyte lineage in a sample, comprising: a) contacting a biological sample with i) a nucleic acid molecule having a sequence that is complementary to nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof, and ii) a nucleic acid molecule having a sequence that is complementary to the at least one other nucleic acid molecule or part thereof; and b) determining whether the nucleic acid molecules bind to the nucleic acid molecules in the sample.
28. A method of screening for the presence of a peptide or polypeptide encoded by a nucleic acid molecule of any one of claims 1 to 4, or a part or variant thereof, and at least one other polypeptide which is a cell marker commonly used to identify cells of melanocyte lineage in a sample, comprising: a) contacting a biological sample with i) an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of any one of claims 1 to 4, or a part or variant thereof, and ii) an antibody that specifically binds to the at least one other polypeptide; and b) determining whether the antibodies bind to their corresponding polypeptides in the sample.
29. A method of diagnosing and/or detecting skin cancer or skin condition comprising: a) contacting a biological sample with a nucleic acid having a complementary sequence to nucleic acid sequence selected from SEQ. ID. No. 1,
SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof; and b) detecting localisation of the nucleic acid as an indicator of the presence (and/or type) of skin cancer or skin condition.
30. A method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of any one of claims 1 to 4, or a part or variant thereof; and b) detecting localisation of the antibody as an indicator of the presence (and/or type) of skin cancer or skin condition.
31. A method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with a nucleic acid having a complementary sequence to nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof, and one or more other nucleic acids complementary to a nucleic acid molecule encoding a marker commonly used to identify cells of melanocyte lineage, or part thereof; and b) determining localisation of the nucleic acids as an indicator of the presence (and/or type) of skin cancer or skin condition.
32. A method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of any one of claims 1 to 4, or a part or variant thereof, and at least one other antibody that binds to a polypeptide that is a marker commonly used to identify cells of melanocyte lineage, or part thereof and b) determining localisation of the antibodies as indicator of the presence (and/or type) of skin cancer or skin condition.
33. A method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with a panel of nucleic acid molecules, or parts thereof, encoding a marker commonly used to identify cells of melanocyte lineage, and a nucleic acid molecule of any one of claims 1 to 4, or a part or variant thereof; and b) determining localisation of the nucleic acid molecules as an indicator of the presence (and/or type) of skin cancer or skin condition.
34. A method of detecting and/or diagnosing skin cancer or skin condition comprising: a) contacting a biological sample with a panel of antibodies that bind specifically to a marker commonly used to identify cells of melanocyte lineage, or part thereof, and a peptide or polypeptide encoded by a nucleic acid molecule of any one of claims 1 to 4, or a part or variant thereof; and b) determining localisation of the antibodies as indicator of the presence (and/or type) of skin cancer or skin condition.
35. The method of any one of claims 26 to 34, wherein the biological sample is selected from the group consisting of a tissue biopsy, a biological fluid and a surgical specimen.
36. The method of any one of claims 26 to 35, wherein the detection or diagnosis is performed in vivo or ex vivo.
37. The method of any one of claims 30 to 36, wherein the skin cancer is melanoma.
38. The method of any one of claims 30 to 37, wherein the skin condition is a disorder of pigmentation, and/or abnormal function, localisation or growth of melanocytes.
39. A method of modulating expression of genes associated with skin cancer or skin condition comprising contacting a cell with a short interfering nucleic acid molecule directed against a nucleic acid sequence selected from SEQ. ID. No. I5 SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No.
7, and SEQ. ID. No. 8, or part thereof.
40. The method of claim 39, wherein the short interfering nucleic acid molecule is selected from a group consisting of short interfering RNA, double stranded RNA, micro RNA and short hairpin DNA.
41. A method of modulating expression of genes associated with skin cancer or skin condition comprising contacting the cells with an antisense nucleic acid molecule directed against a nucleic acid sequence selected from SEQ. ID. No. 1, SEQ. ID. No. 2, SEQ. ID. No. 4, SEQ. ID. No. 5, SEQ. ID. No. 6, SEQ. ID. No. 7, and SEQ. ID. No. 8, or part thereof.
42. Use of a nucleic acid molecule comprising a nucleic acid molecule of any one of claims 1 to 4, or a part or variant thereof, or an inhibitory or interfering RNA or DNA sense or antisense sequence, or an antibody that specifically binds to a peptide or polypeptide encoded by a nucleic acid molecule of any one of claims 1 to 4, or a part or variant thereof, or a protein comprising said peptide or polypeptide, in the treatment of disorders associated with melanoma and/or disorders of pigmentation, and/or abnormal function, localisation or growth of melanocytes.
43. Use according to claim 42, wherein the disorders of pigmentation is selected from hypo -pigmentation and/or hyper-pigmentation.
44. A method of modulating expression of genes associated with changes in skin pigmentation or cosmetic lightening or darkening of skin tone, comprising contacting a cell with an inhibitory or interfering RNA or DNA, sense or antisense, sequence directed against a nucleic acid molecule of any one of claims 1 to 4, or a part or variant thereof.
45. A method according to any one of claims 24, 42 or 44 wherein the inhibitory or interfering RNA is an siRNA.
46. A method according to claim 40 or claim 45, wherein the siRNA is selected from nucleic acid sequences 5 ' -GUAUCUTACUCATAUGCUUtt-S ' or 5 ' - AAGCAUGUGAGUGAGAU ACt c- 3 ' or 5 ' -CUUUGCACAGCAAUAAACUtt- 3 ' or 5 ' -AGUUUAUUGCUGUGCAAAGt g- 3 ' .
47. A nucleic acid molecule encoding a protein having SEQ. ID. No. 3, comprising 3 ' and 5' regulatory regions.
48. A method according to any one of claims 27, 28, 31, 32 or 34, wherein the cell marker is selected from melanA, gplOO, tyrosinase, trp-1 and trp-2.
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Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2010098682A1 (en) * 2009-02-27 2010-09-02 Auckland Uniservices Limited Cell marker for melanocyte lineage and cancer cells and uses thereof

Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0110716A2 (en) * 1982-11-30 1984-06-13 Sloan-Kettering Institute For Cancer Research Monoclonal antibodies against melanocytes and melanomas
WO2004018675A1 (en) * 2002-08-21 2004-03-04 The University Of British Columbia Treatment of melanoma by reduction in clusterin levels
US20060025363A1 (en) * 2002-08-21 2006-02-02 Ute Breitenbach Use of antisense oligonucleotides for the treatment of degenerative skin conditions
WO2006048291A2 (en) * 2004-11-03 2006-05-11 Almac Diagnostics Limited Transcriptome microarray technology and methods of using the same
US20070083334A1 (en) * 2001-09-14 2007-04-12 Compugen Ltd. Methods and systems for annotating biomolecular sequences
US20070161031A1 (en) * 2005-12-16 2007-07-12 The Board Of Trustees Of The Leland Stanford Junior University Functional arrays for high throughput characterization of gene expression regulatory elements

Family Cites Families (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001000874A2 (en) * 1999-06-30 2001-01-04 Ludwig Institute For Cancer Research Cancer associated antigens and uses therefor
US20020110815A1 (en) * 2000-04-14 2002-08-15 James Lillie Novel genes, compositions and methods for the identification, assessment, prevention, and therapy of human cancers
WO2002064626A2 (en) * 2000-10-27 2002-08-22 Pe Corporation (Ny) Isolated human secreted proteins, nucleic acid molecules encoding human secreted proteins, and uses thereof
WO2004093804A2 (en) * 2003-04-18 2004-11-04 Five Prime Therapeutics, Inc. Human polypeptides encoded by polynucleotides and methods of their use

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0110716A2 (en) * 1982-11-30 1984-06-13 Sloan-Kettering Institute For Cancer Research Monoclonal antibodies against melanocytes and melanomas
US20070083334A1 (en) * 2001-09-14 2007-04-12 Compugen Ltd. Methods and systems for annotating biomolecular sequences
WO2004018675A1 (en) * 2002-08-21 2004-03-04 The University Of British Columbia Treatment of melanoma by reduction in clusterin levels
US20060025363A1 (en) * 2002-08-21 2006-02-02 Ute Breitenbach Use of antisense oligonucleotides for the treatment of degenerative skin conditions
WO2006048291A2 (en) * 2004-11-03 2006-05-11 Almac Diagnostics Limited Transcriptome microarray technology and methods of using the same
US20070161031A1 (en) * 2005-12-16 2007-07-12 The Board Of Trustees Of The Leland Stanford Junior University Functional arrays for high throughput characterization of gene expression regulatory elements

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
DATABASE EMBL 3 March 2004 (2004-03-03), "13 kDa Protein", XP008135882, Database accession no. IPI00401915 *
DATABASE GENBANK [online] 16 September 2003 (2003-09-16), "Homo sapiens hypothetical protein LOC146481, mRNA", XP008135880, Database accession no. BC023607 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2010098682A1 (en) * 2009-02-27 2010-09-02 Auckland Uniservices Limited Cell marker for melanocyte lineage and cancer cells and uses thereof

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