JP2005536981A - Methods and compositions for diagnosing cancer susceptibility and defective DNA repair mechanisms, and methods and compositions for treating them - Google Patents

Abstract

Methods and compositions for diagnosing cancer susceptibility, defective DNA repair mechanisms, and methods and compositions for treating them are provided. Among the sequences provided herein, the FANCD2 gene has been identified, and probes and primers are provided for screening patients in gene-based tests and for diagnosing Fanconi anemia and cancer. The FANCD2 gene can be targeted in vivo to prepare experimental mouse models for use in screening novel therapeutics to treat conditions associated with defective DNA repair. The FANCD2 polypeptide has been sequenced and proven to exist as two isoforms identified as FANCD2-S and monoubiquitinated FANCD-L. Antibodies including polyclonal and monoclonal antibodies that discriminate between the two isoforms have been prepared and used in diagnostic tests to determine whether a subject has an intact Fanconi anemia / BRCA pathway.

Description

Government support The work described here was supported by the National Institutes of Health (NIH) grant numbers RO1HL52725-04, RO1DK43889-09, 1PO1HL48546, and PO1HL54785-04 . The US government has certain rights to the invention.

BACKGROUND The present invention relates to diagnosis of cancer susceptibility in a subject having a defect in the FANCD2 gene and determination of an appropriate treatment protocol for the subject who has developed cancer. Using animal models that are defective in the FANCD2 gene, therapeutic agents can be screened.

  Fanconi anemia (FA) is an autosomal recessive cancer susceptibility syndrome characterized by congenital defects, bone marrow failure and a predisposition to cancer. FA patient-derived cells exhibit unique hypersensitivity to substances that produce interstrand DNA crosslinks such as mitomycin C or diepoxybutane. FA patients develop several types of cancer, including acute myeloid leukemia and skin, gastrointestinal and gynecological cancers. Skin and gastrointestinal tumors are usually squamous cell carcinomas. At least 20% of FA patients develop cancer. The average age at which patients develop cancer is 15 years for leukemia, 16 years for liver tumors, and 23 years for other tumors. (D'Andrea et al., Blood, (1997) vol. 90, p1725, Garcia-Higuera et al., Curr. Opin. Hematol., (1999) vol. 2, p83-88, and Heijna et al., Am. J. Hum. Genet.vol.66, p1540-1551).

  FA is genetically heterogeneous. In somatic cell fusion studies, at least seven distinct complementarity groups have been identified (Joenje et al., (1997) Am. J. Hum. Genet., Vol. 61, p940-944, and Joenje et al., (2000). Am. J. Hum. Genet, vol. 67, p759-762). This observation led to the hypothesis that the FA gene defines a multi-component pathway that is involved in cellular responses to DNA cross-linking. Five FA genes (FANCA, FANCC, FANCE, FANCF and FANCG) have been cloned and FANCA, FANCC and FANCG proteins have been demonstrated to form molecular complexes primarily with nuclear localization. FANCC is also localized in the cytoplasm. Various FA proteins have little or no known sequence motifs in invertebrate species, without strong homologues of FANCA, FANCC, FANCE, FANCF, and FANCG proteins. FANCF has a weak homology of unknown significance to E. coli RNA binding protein. The two complementarity groups most frequently seen are FA-A and FA-C, which together account for 75-80% of FA patients. Multiple mutations are recognized in the FANCA gene, which spans 80 kb and consists of at least 43 exons. FANCC has been found to have 14 exons and spans approximately 80 kb. The number of mutations within the FANCC gene has been identified, which correlates with FAs of varying severity. FA-D has been identified as a distinct but rare complementation group. Although FA-D patients can be distinguished from other subtypes of patients by phenotype, FA protein complexes usually assemble into FA-D cells (Yamashita et al. (1998) PNA). S., vol. 95, p13085-13090).

  Cloned FA proteins encode orphan proteins that do not have sequence similarity with each other or with other proteins in GenBank, in which functional domains are not evident. Little is known about the cellular or biochemical functions of these proteins.

  The diagnosis of FA is complicated by wide variability in the FA patient phenotype. To further confound the diagnosis, approximately 33% of FA patients have no apparent congenital abnormalities. Moreover, current diagnostic tests cannot distinguish FA carriers from the general population. Problems related to diagnosis are described in D'Andrea et al. (1997). Numerous cell phenotypes have been reported in FA cells, but the most consistent is hypersensitivity to bifunctional alkylating agents such as mitomycin C or diepoxybutane. These agents produce interstrand DNA crosslinks (an important type of DNA damage).

  Diagnosis of cancer susceptibility is complicated by the numerous regulatory genes and biochemical pathways involved in cancer formation. The various cancers and associated genetic lesions that depend on how they develop can determine how the subject responds to any particular therapeutic treatment. Genetic lesions associated with defective repair mechanisms can result in defective cell division and apoptosis, which in turn can increase the patient's susceptibility to cancer. FA is a disease state in which a number of pathological outcomes are associated with defective repair mechanisms in addition to cancer susceptibility.

  An understanding of the molecular genetics and cell biology of the Fanconi anemia pathway provides insights into prognosis, diagnosis, and treatment of pathologies associated with defects in certain types of cancer and DNA repair mechanisms that occur in non-FA patients and FA patients Is obtained.

SUMMARY OF THE INVENTION The invention features a method of diagnosing or determining whether a patient has cancer or whether the patient is at increased risk of developing cancer, said method comprising Fanconi anemia / BRCA for the presence of a cancer-related defect. Testing for pathway genes, wherein the presence of one or more cancer-related defects is indicative of an increased risk of cancer or cancer in the patient. The cancer may be breast cancer, ovarian cancer, or prostate cancer, or other forms of cancer. A cancer-related defect results in a decrease in the ratio of FANCD2-L to FANCD2-S compared to the ratio in patients who do not have one or more cancer-related defects in the Fanconi anemia / BRCA pathway gene It may be a sex defect.

  The invention also features a method of diagnosing or determining whether a patient has cancer or whether the patient is at increased risk of developing cancer, said method comprising a Fanconi anemia / BRCA pathway protein for the presence of a cancer-related defect Wherein the presence of the cancer-related defect indicates an increase in cancer or cancer risk in the patient. The cancer may be breast cancer, ovarian cancer, or prostate cancer, or other forms of cancer.

  In another aspect, the invention features a method of diagnosing or determining whether a patient has an increased risk of carcinogenesis, the method comprising: (a) providing a tissue sample from the patient; b) inducing DNA damage in cells of the tissue sample; and (c) assaying for the presence of FANCD2-S and FANCD2-L protein in the cells, wherein FANCD2-L A decrease in the ratio of FANCD2-S indicates that the patient has an increased risk of carcinogenesis. The cancer may be breast cancer, ovarian cancer, or prostate cancer, or other forms of cancer. Patients may or may not have any previously known cancer-related defects in the BRCA-1 or BRCA-2 genes. Multiple such tissue samples can be distributed on or within the array.

  In another aspect, the invention features a method for determining whether a patient has cancer or whether the patient has an increased risk of carcinogenesis, wherein the patient is BRCA-1 or BRCA- No known cancer causing a defect in two genes, the method comprising: (a) providing a DNA sample from the patient; and (b) a FANCD2 gene specific polyseq. Amplifying the patient-derived FANCD2 gene using nucleotide primers; (c) sequencing for the amplified FANCD2 gene; and (d) the patient-derived FANCD2 gene sequence as a reference FANCD2 gene sequence. Where the mismatch between the two gene sequences is a cancer-related deficiency. Indicates the presence of the presence of one or more cancer-associated defects, it said patient is a cancer, or the patient's cancer risk to indicate that has increased. The cancer may be breast cancer, ovarian cancer, or prostate cancer, or other forms of cancer. The patient may or may not have any previously known cancer-related defect in the BRCA-1 or FANC-D1 / BRCA-2 gene. Multiple such tissue samples can be distributed on or within the array. As shown in Table 7, SEQ ID NOS: 115 to 186 are matched primer sets, odd numbered primers are forward primers, and even numbered primers are reverse primers. Primers can also be used from various pairs to create a new primer pair, eg, SEQ ID NO: 115 can be used with SEQ ID NO: 118. By “discrepancy” is meant a difference between two sequences, which is known to be associated with cancer.

  In yet another aspect, the invention features a method of screening a chemical sensitizer, the method comprising: (a) providing a potential inhibitor of Fanconi anemia / BRCA pathway; (b) 1 Providing a tumor cell line that is resistant to the anti-tumor agent; and (c) contacting the tumor cell line, the potential inhibitor of the Fanconi anemia / BRCA pathway, and one or more of the anti-tumor agents. And (d) measuring the growth rate of the tumor cell line in the presence of the inhibitor of the Fanconi anemia / BRCA pathway and the antitumor agent, wherein the presence of the antitumor agent A decrease in the growth rate of the tumor cell line compared to cells of the tumor cell line in the absence and in the absence of the inhibitor of the Fanconi anemia / BRCA pathway is attributed to the potential inhibitor. Shows that it is a sensitizer. Potential inhibitors of the Fanconi anemia / BRCA pathway can be screened on a microarray, where the microarray contains an address containing one or more cells that are resistant to one or more anti-tumor agents. A potential inhibitor of the Fanconi anemia / BRCA pathway may be an inhibitor of FANCD2 protein ubiquitination. The anti-tumor agent may be cisplatin. The tumor cell line may be an ovarian cancer cell line.

  In another aspect, the invention features a method of treating a patient having cancer, wherein the cancer is resistant to an anti-tumor agent, said method comprising inhibiting a therapeutically effective amount of the Fanconi anemia / BRCA pathway Administering an agent together with said antitumor agent. The anti-tumor agent may be cisplatin. A potential inhibitor of the Fanconi anemia / BRCA pathway may be an inhibitor of FANCD2 protein ubiquitination. The tumor cell line may be an ovarian cancer cell line.

  In yet another aspect, the invention features a method of screening for a cancer therapeutic agent, the method comprising: (a) one or more containing a Fanconi anemia / BRCA pathway gene having one or more cancer-related defects. Providing cells; (b) growing the cells in the presence of a potential cancer therapeutic; and (c) a growth rate of corresponding cells grown in the absence of the potential cancer therapeutic. Determining the proliferation rate of the cells in the presence of the potential cancer therapeutic agent as compared to, wherein the proliferation rate of the corresponding cells grown in the absence of the potential cancer therapeutic agent A decrease in the proliferation rate of the cells in the presence of the potential cancer therapeutic agent compared to the above indicates that the potential cancer therapeutic agent is a cancer therapeutic agent. The cells may contain Fanconi anemia / BRCA pathway genes with one or more cancer-related defects, or several such genes, and are distributed in the array.

  The invention also features a method of predicting the effectiveness of a therapeutic agent in a cancer patient, the method comprising: (a) providing a tissue sample from the cancer patient being treated with the therapeutic agent; (B) inducing DNA damage in the cells of the tissue sample; and (c) detecting the presence of FANCD2-L protein in the cells, wherein the presence of FANCD2-L Indicates a decrease in the effectiveness of the therapeutic agent in the cancer patient. The therapeutic agent may be an antitumor agent, for example cisplatin. Alternatively, in step (c), both FANC-D2-S and FANC-D2-L can be detected, and a decrease in the ratio of FANCD2-L to FANCD2-S compared to the ratio in non-cancer patients is effective. Deterioration of sex.

  The invention also features a method for determining resistance of tumor cells to an anti-tumor agent, comprising: (a) providing a tissue sample from a patient being treated with the anti-tumor agent; Inducing DNA damage in cells of the tissue sample; and (c) determining the methylation status of the Fanconi anemia / BRCA pathway gene; wherein the methylation of the Fanconi anemia / BRCA pathway gene is Shows resistance of tumor cells to antitumor agents. The Fanconi anemia / BRCA gene may be the FANCF gene. The anti-tumor agent may be cisplatin.

  The invention also features a kit for detecting a defect in the FANCD2 gene comprising a polynucleotide primer pair specific for the FANCD2 gene, a reference FANCD2 gene sequence, and packaging material therefor.

  The invention also features a kit for detecting the presence of FANCD2-L, comprising a FANCD2-L specific antibody and packaging material therefor.

  The invention also features a kit for determining the methylation status of a Fanconi anemia / BRCA pathway gene, comprising a FANCD2 polynucleotide primer pair and probe, a control unmethylated control FANCD2 gene sequence, and packaging material therefor And

  The invention also features a kit for screening for chemical sensitizers comprising a tumor cell line resistant to one or more anti-tumor agents and packaging materials therefor. The tumor cell line may be an ovarian cancer cell line, such as a cisplatin resistant ovarian cancer cell line. The anti-tumor agent may be cisplatin.

  The invention also features a microarray containing one or more nucleic acid sequences from one or more Fanconi anemia / BRCA pathway genes. The gene can be selected from the group consisting of ATM, FANCA, FANCB, FANCC, FANCD1, FANCD2, FANCE, FANCF and FANCG.

  The invention also features the use of the microarray in a method for determining whether a patient has cancer or whether the patient has an increased risk of developing cancer, the method comprising: (a) providing the microarray (B) providing a nucleic acid sample from the patient; (c) hybridizing the nucleic acid sample to the nucleic acid sequence from the Fanconi anemia / BRCA pathway on the microarray; and (d) Detecting the presence of a mutation in the Fanconi anemia / BRCA pathway gene in a patient-derived nucleic acid sample, wherein the detection of the presence of the mutation increases the risk of developing cancer or a patient with cancer. Showing patients.

  In one embodiment of the invention, (a) a nucleotide sequence encoding a polypeptide having the amino acid sequence shown in SEQ ID NO: 4; (b) a nucleotide sequence that is at least 90% identical to the polynucleotide of (b); (C) a nucleotide sequence that is complementary to the polynucleotide of (b); (d) a nucleotide sequence that is at least 90% identical to the nucleotide sequence set forth in SEQ ID NOs: 5-8, 187-188; and (e) An isolated nucleic acid molecule is provided comprising a polynucleotide selected from: a nucleotide sequence that is complementary to the nucleotide sequence of (d). The polynucleotide may be an RNA molecule or a DNA molecule such as cDNA.

  In another embodiment of the invention, the amino acid sequence of SEQ ID NO: 4 is sufficient to maintain the biological properties of FANCD2 conversion from short to long form in the cell nucleus to promote DNA repair. An isolated nucleic acid molecule consisting essentially of a nucleotide sequence encoding a polypeptide having an amino acid sequence similar to is provided. Alternatively, the isolated nucleic acid molecule is essentially complementary to a polynucleotide having a nucleotide sequence that is at least 90% identical to SEQ ID NOs: 9-191 or a nucleotide sequence that is at least 90% identical to SEQ ID NOs: 9-191 A polynucleotide which is

  In certain embodiments, a method is provided for making a recombinant vector comprising inserting any of the isolated nucleic acid molecules described above into the vector. By this method, a recombinant vector product can be produced, and the vector can be introduced into a host cell to produce a recombinant host cell.

  In certain embodiments of the invention, a method of creating a FA-D2 cell line, comprising: (a) obtaining a cell from a subject having a biallelic mutation in a complementation group associated with FA-D2; And (b) infecting the cells with a transforming virus to create a FA-D2 cell line, wherein the cells are selected from fibroblasts and lymphocytes, and the transforming virus is Epstein-Barr virus And a method selected from retroviruses. The FA-D2 cell line can be obtained, for example, by performing a diagnostic assay selected from (i) Western blotting or nuclear immunofluorescence using antibodies specific for FANCD2 and (ii) DNA hybridization assays. It can be characterized by determining the presence of defective FANCD2 in the cell line.

  In certain embodiments of the invention, there is provided a recombinant method for producing a polypeptide comprising culturing a recombinant host cell, said host cell comprising any of the isolated nucleic acid molecules described above. .

  In certain embodiments of the invention, (a) SEQ ID NO: 4; (b) an amino acid sequence that is at least 90% identical to (a); (c) at least one of SEQ ID NOs: 5-8, 187-188 and at least An amino acid sequence encoded by a polynucleotide having a nucleotide sequence that is 90% identical; and (d) a nucleotide sequence that is at least 90% identical to a sequence complementary to at least one of SEQ ID NOs: 5-8, 187-188 An amino acid sequence encoded by the polynucleotide having; and (e) a polypeptide fragment of (a)-(d), a fragment that is at least 50 amino acids in length; An isolated polypeptide is provided.

  The isolated polypeptide can be encoded by DNA having a mutation selected from nt 376A-G, nt 3707G-A, nt 904C-T and nt 958C-T. Alternatively, the polypeptide can be characterized by a polymorphism in the DNA encoding the polypeptide, the polymorphism being nt 1122A-O, nt 1440T-C, nt 1509C-T, nt 2141C-T, nt 2259T to C, nt 4098T to G, nt 4453G to A. Alternatively, the polypeptide can be characterized by a mutation at amino acid 222 or amino acid 561.

  In one embodiment of the invention, the preparation of an antibody having binding specificity for FANCD2 protein is described, wherein said antibody may be a monoclonal antibody or a polyclonal antibody, wherein FANCD2 is FANCD2-S or FANCD2-L. It may be.

  In certain embodiments of the invention, a diagnostic method for measuring FANCD2 isoforms in a biological sample is provided, wherein the method comprises: (a) treating the sample with a first complex with FANCD2-L. Exposing to a first antibody to form a body and optionally to a second antibody to form a second complex with FANCD2-S; and (b) using a marker in the sample Detecting the amount of the first complex and the second complex. The sample may be intact cells or lysed cells in lysate. The biological sample may be from a human subject who has hypersensitivity to cancer or who has an early stage cancer. The sample may be derived from a cancer in a human subject, wherein said cancer is melanoma, leukemia, astrocytoma, glioblastoma, lymphoma, glioma, Hodgkin lymphoma, chronic lymphocytic leukemia and Selected from pancreatic cancer, breast cancer, thyroid cancer, ovarian cancer, uterine cancer, testicular cancer, pituitary cancer, kidney cancer, gastric cancer, esophageal cancer and rectal cancer. The biological sample can be from a human fetus or a human adult, and can be from any of a blood sample, a biopsy tissue sample, and a cell line from a subject. The biological sample may be from the heart, brain, placenta, liver, skeletal muscle, kidney, pancreas, spleen, thymus, prostate, testis, uterus, small intestine, colon, peripheral blood or lymphocytes. The marker may be a fluorescent marker, optionally a fluorescent marker conjugated with FANCD2-L antibody, optionally a chemiluminescent marker conjugated with FANCD2-L antibody, and the first and second complexes are conjugated to the substrate. It can be conjugated to a third antibody. If the sample is a lysate, the sample can be subjected to a separation method to separate FANCD2 isoforms, and the separated isoforms can be identified by determining binding to the first or second FANCD2 antibody.

  In certain embodiments of the invention, selecting an antibody against a FANCD2 protein and determining whether the amount of FANCD2-L isoform is reduced in said cell population as compared to the amount in a wild type cell population. A diagnostic test to identify a defect in the Fanconi anemia pathway within a cell population from a subject, but if the amount of FANCD2-L protein is reduced, a wild-type cell population Determining whether the amount of any of FANCA, FANCB, FANCC, FANCD1, FANCE, FANCF or FANCG protein is altered in the cell population as compared to Can be identified. In one example, the amount of isoform depends on the separation of FANCD2-L and FANCD2-S isoforms, where the separation is by gel electrophoresis or migration binding banded test strip. Can be achieved.

  In certain embodiments of the invention, selecting a cell population in which FAND2-L is produced in reduced amounts; exposing the cell population to individual members of a candidate therapeutic molecule library; and within the cell population A screening assay for identifying therapeutic agents is provided comprising identifying individual member molecules that induce an increase in the amount of FANCD2-L. In one example, the cell population is an in vitro cell population. In another example, the cell population is an in vivo cell population, the in vivo cell population is in an experimental animal, and the experimental animal has a mutated FANCD2 gene. In yet another example, the experimental animal is a knockout mouse in which the mouse FAND2 gene is replaced with a human mutant FANCD2 gene. In another example, a chemical carcinogen is added to a cell population in which FANCD2 is produced in a reduced amount, and any member molecule increases the amount of FANCD2-L so that the cells can be protected from the adverse effects of the chemical carcinogen. Whether it can be triggered.

  In certain embodiments of the invention, an experimental animal model is provided in which the animal FANCD2 gene has been removed and optionally replaced with any of the nucleic acid molecules described above.

  In one embodiment of the invention, a method for identifying a mutant FANCD2 nucleotide sequence within a suspected mutant FANCD2 allele in a cell sample from a subject, wherein the nucleotide sequence of the suspected mutant FANCD2 allele is wild-type. A method is provided comprising a step comprising comparing to a type FANCD2 nucleotide sequence, wherein the difference between the suspected mutant sequence and the wild type sequence identifies the mutant FANCD2 nucleotide sequence in the cell sample. In one example, the suspected mutant allele is a germline allele. In yet another example, identification of a mutated FANCD2 nucleotide sequence is useful in diagnosing an increased risk for a subject having a predisposition to cancer or a progeny with Fanconi anemia in the subject. In another example, the suspected mutant allele is a somatic allele in the tumor type, and the step of identifying the mutant FANCD2 nucleotide sequence is useful for diagnosis of the tumor type. In another example, the wild-type nucleotide sequence and the suspected mutant FANCD2 nucleotide sequence are selected from genes, mRNA and cDNA made from mRNA. In another example, comparing the polynucleotide sequence of a suspected mutant FANCD2 allele to a wild type FANCD2 polynucleotide sequence, selecting a FANCD2 probe that specifically hybridizes to the mutant FANCD2 nucleotide sequence; and Detecting the presence of the mutant sequence by hybridization with a probe. In another example, comparing the polynucleotide sequence of a suspected mutant FANCD2 allele with a wild type FANCD2 polynucleotide sequence is a primer set specific for wild type FANCD2 DNA to produce amplified FANCD2 DNA. Amplifying all or part of the FANCD2 gene using and sequencing the FANCD2 DNA so that the mutant sequence can be identified. In another example, if the mutant FANCD2 nucleotide sequence is a germline change within a FANCD2 allele of a human subject, the change is selected from the changes listed in Table 3, and the mutant FANCD2 nucleotide sequence is If the change is a somatic cell within the FANCD2 allele of the human subject, the change is selected from the changes listed in Table 3.

  In one embodiment of the present invention, a method for diagnosing susceptibility to cancer in a subject, wherein the germline sequence of the FANCD2 gene or the mRNA sequence thereof in a tissue sample from the subject is the germline of the FANCD2 gene. A method is provided comprising a step comprising comparing the sequence or its mRNA sequence, wherein a change in the germline sequence of the subject FANCD2 gene or its mRNA sequence is indicative of susceptibility to the cancer. Changes can be detected in the regulatory region of the FANCD2 gene. Changes in the germline sequence consisted of (a) observing a change in electrophoretic mobility of single stranded DNA on a non-denaturing polyacrylamide gel; and (b) a FANCD2 gene probe was isolated from a tissue sample. Hybridizing to genomic DNA; (c) hybridizing an allele-specific probe to genomic DNA of the tissue sample; (d) all or one of the FANCD2 genes from the tissue sample to generate an amplified sequence. (E) amplifying all or part of the FANCD2 gene from a tissue sample using primers for a specific FANCD2 mutant allele; f) FA from tissue samples to generate cloned sequences Molecularly cloning all or part of the CD2 gene and sequencing for the cloned sequence; (g) (i) FANCD2 gene or FANCD2 mRNA isolated from a tissue sample; and (ii) human wild type FANCD2 Identifying a mismatch between molecules (i) and (ii) when a nucleic acid probe complementary to the gene sequence hybridizes to each other to form a duplex; (h) in a tissue sample; Amplifying the FANCD2 gene sequence in the tissue sample and hybridizing the nucleic acid probe comprising the wild type FANCD2 gene sequence to the nucleic acid probe; and (i) amplifying the FANCD2 gene sequence in the tissue sample and Hybridizer containing amplified sequence to nucleic acid probe (J) screening for deletion mutations in the tissue sample; (k) screening for point mutations in the tissue sample; and (l) screening for insertion mutations in the tissue sample. And (m) in situ hybridizing the FANCD2 gene of the tissue sample with a nucleic acid probe comprising the FANCD2 gene; and an assay selected from the group consisting of:

  In one embodiment of the invention, a method of diagnosing susceptibility to cancer in a subject comprising: (a) obtaining genetic material from the subject so that a defective DNA repair can be determined; and (b) a gene. Determining the presence of a mutation in the set, the set comprising FAND2 and at least one of FANCA, FANCB, FANCC, FANCD1, FANCDE, FANDF, FANDG, BRACA1 and ATM; and ( c) diagnosing susceptibility to cancer from the presence of a mutation within said gene set.

  In one embodiment of the present invention, a method of detecting a mutation in a tumor lesion with a FANCD2 gene in a human subject comprising: Comparing to the sequence of the gene or its mRNA, wherein a change in the sequence of the subject FANCD2 gene or its mRNA is indicative of a mutation in the FANCD2 gene of the tumor lesion A method is provided. A therapeutic protocol can be provided for treating tumor lesions due to mutations in the FANCD2 gene of the tumor lesions.

  In one embodiment of the present invention, a method for confirming the absence of a FANCD2 mutation in a tumor lesion from a human subject, wherein the sequence of the FANCD2 gene or the mRNA sequence thereof in the subject lesion-derived tissue sample A method is provided comprising the step of comparing to the sequence of the FANCD2 gene or its mRNA, wherein the presence of a wild type sequence in the tissue sample indicates a lack of mutation in the FANCD2 gene .

  In one embodiment of the invention, a method for determining a treatment protocol for a subject having cancer, comprising: Determining whether it occurs in a subject-derived cell sample; and (b) if a defect is detected in (a), determining whether the defect is the result of a genetic defect in a non-cancer cell. Reducing the use of a treatment protocol that induces an increase in DNA damage to protect normal tissue in the subject if and (c) (b) is positive, and (b) is negative If the defect is only contained within a genetic defect in the cancer cell, increase the DNA damage so that it can adversely affect the cancer cell. Step of increasing the use of treatment protocols emanating; method and a is provided.

  In certain embodiments of the invention, there is provided a method of treating a FA pathway defect in a cellular target comprising: administering to the target an effective amount of a FANCD2 protein or exogenous nucleic acid. The FA pathway defect may be a defective FANCD2 gene and the exogenous nucleic acid vector may further comprise introducing a vector according to those described above. The vector can be selected from a mutant herpesvirus, an E1 / E4 deleted recombinant adenovirus, a mutant retrovirus, said virus vector being essentially related to a viral gene for producing infectious novel viral particles. There is a defect. The vector may be contained in a lipid micelle.

  In one embodiment of the invention, a method for treating a patient having a defective FANCD2 gene, as set forth in SEQ ID NO: 4 to functionally cure a defect arising from a condition resulting from a defective FANCD2 gene A method is provided that includes providing a polypeptide.

  In certain embodiments of the invention, a cell-based assay for detecting a FA pathway defect comprising: obtaining a cell sample from a subject; exposing the cell sample to a DNA damaging agent; and FANCD2. -Detecting whether L is up-regulated, wherein the lack of up-regulation indicates FA pathway defects; In cell-based assays, the amount of FANCD2 is: immunoblotting to detect nuclear foci; Western blot to detect the amount of FANCD2 isoform; and quantification of mRNA by hybridizing with a DNA probe; And can be measured by an analytical technique selected from

  In one embodiment of the invention, a kit for use in detecting cancer cells in a biological sample comprising: (a) a primer pair that binds to a sequence in the FANCD2 gene under high stringency conditions. A kit comprising: a primer pair selected to specifically amplify the altered nucleic acid sequence set forth in Table 7; and a container for each of said primers.

  As used herein, “Fanconi Anemia / BRCA pathway” or “Fanconi Anemia Pathway” refers to 7 complementarity groups (FA-A to FA-G). Refers to the genes, BRCA-1 and ATM genes, and their respective proteins that interact in a pathway referred to herein as the Fanconi anemia / BRCA pathway and regulate cellular responses to DNA damage (see FIG. 22) ).

The genes for the Fanconi anemia / BRCA pathway are as follows:
1) FANC-A (eg, Genbank accession number: NM) 000135)
2) FANC-B (not yet cloned)
3) FANC-C (eg, Genbank accession number: NM) 000136)
4) FANC-D1 / BRCA-2 (eg, Genbank accession number: U43746)
5) FANC-D2 (eg, Genbank accession number: NM) 030884)
6) FANC-E (eg, Genbank accession number: NM) 021922)
7) FANC-F (eg, Genbank accession number: NM) 022725)
8) FANC-G (eg, Genbank accession number: BC000034)
9) BRCA-1 (eg, Genbank accession number: U14680)
10) ATM (eg, Genbank accession number: U33841)

  “Testing a Fanconi Anemia / BRCA pathway of the presence of the cancer-associated doc”, as used herein. A method for determining whether a protein encoded by a Fanconi anemia / BRCA pathway gene as defined in claim 1 induces cancer or has a defect associated with cancer as defined herein. means.

  As used herein, the term “defect” refers to any gene or protein in the Fanconi anemia / BRCA pathway and / or any of the proteins in the Fanconi anemia / BRCA pathway. It means change.

  “Alternation” of a gene: a) changes in the DNA sequence itself, ie, DNA mutations, deletions, insertions, substitutions; b) DNA that affects the regulation of gene expression such as regulatory region mutations Modifications, modifications in the associated chromatin, modifications of intron sequences that affect mRNA splicing, modifications that affect the methylation / demethylation status of gene sequences; and c) affect protein translation or mRNA transport or mRNA splicing. But not limited thereto.

  Protein "changes" include amino acid deletions, insertions, substitutions; modifications that affect protein phosphorylation or glycosylation; modifications that affect protein transport or localization; one or more related proteins and proteins Modifications that affect the ability to form a complex, or changes in amino acid sequence caused by changes in the DNA sequence encoding an amino acid include, but are not limited to.

  As used herein, the term “increased risk” or “elevated risk” refers to a patient that does not have a change in a Fanconi anemia / BRCA pathway gene or protein, It means higher cancer incidence in patients with altered Fanconi anemia / BRCA pathway genes or proteins. “Increased risk” also means patients who have already been diagnosed with cancer and may have increased the incidence of different forms of cancer. According to the present invention, an “increased risk” of cancer is 50%, preferably 90% in the probability of acquiring cancer compared to a patient who does not have a cancer-related defect in the Fanconi anemia / BRCA pathway gene. Related to a cancer-related defect in the Fanconi anemia / BRCA pathway gene that results in an increase of%, more preferably 99% or more.

  As used herein, an “inhibitor of the Fanconi Anemia / BRCA pathway” according to the present invention disrupts FANCD2-L protein function either directly or indirectly Any compound is meant. Disruption of FANCD2-L protein function is due to disruption of any other FAN protein upstream of FANCD2 protein in the pathway, inhibition of FANCD2-S ubiquitination to FANCD2-L isoforms, and subsequent FANCD2-L protein Either through inhibition of nuclear transport or disruption of FANCD2-L protein binding to the nuclear BRCA DNA repair protein complex. An “inhibitor” according to the present invention is a nucleic acid (antisense RNA or DNA oligonucleotide), protein (humanized antibody), peptide or peptide that specifically binds to FANCD2-L and disrupts FANCD2-L protein function. It may be a small molecule drug. In the most preferred embodiment, the inhibitor of the Fanconi anemia / BRCA pathway is a small molecule inhibitor of monoubiquitination of the FANCD2 protein.

  As used herein, “reduction in the ratio of FANCD2-L relative to FANCD2-S” is a percentage of the total amount of FANCD2 protein in the FANCD2-L isoform. Means decrease. In certain preferred embodiments, the total amount of FANCD2 protein present in the FANCD2-L isoform is at most 25%, preferably 10%, more preferably 1% and most preferably 0%. Such a decrease indicates a defect in one or more genes or proteins of the Fanconi anemia / BRCA pathway, as defined herein.

  “Testing a Fanconi Anemia / BRCA pathway of the presence of the cancer-associated doc”, as used herein. Proteins encoded within the seven complementarity groups (A, B, C, D, E, F and G), including the Fanconi anemia / BRCA gene pathway, induce cancer or cancer in patients as defined in Means a method to determine if it has a defect or other mutation that contributes to

  As used herein, the term “inducing DNA damage” refers to both chemical and physical methods of damaging DNA. Chemicals that damage DNA include, but are not limited to, ethidium bromide, acridine orange, and acids / bases such as free radicals and various mutagens. Physical methods include, but are not limited to, ionizing radiation such as X-rays and gamma rays, and ultraviolet (UV) radiation. Both methods of “inducing DNA damage” typically include, but are not limited to, single strand breaks, double strand breaks, base changes, DNA strand insertions, deletions or cross-links, Mutations can occur.

  As used herein, the term “tissue biopsy” means a biomaterial isolated from a patient. The term “tissue” as used herein is a cell aggregate that performs a specific function in a living body, for example, biological fluid such as blood, plasma, sputum, urine, cerebrospinal fluid, washing fluid, and white blood cell Includes cell lines and other sources of cellular material, including but not limited to electrophoresis samples.

  The term “amplifying” as used herein, when applied to a nucleic acid sequence, preferably results in one or more copies of the particular nucleic acid sequence from the template nucleic acid by the polymerase chain reaction method. Refers to the process (Mullis and Faloona, 1987, Methods Enzymol., 155: 335). “Polymerase chain reaction” or “PCR” means an in vitro method for amplifying a specific nucleic acid template sequence. A PCR reaction includes a series of repeated temperature cycles, typically performed in a volume of 50-100 μL. The reaction mixture includes dNTPs (each of the four deoxynucleotides dATP, dCTP, dGTP, and dTTP), a primer, a buffer, a DNA polymerase, and a nucleic acid template. The PCR reaction provides a set of polynucleotide primers (the first primer contains a sequence complementary to a region in one strand of a nucleic acid template sequence, ready for the synthesis of a complementary DNA strand, and The second primer contains a sequence complementary to one region in the second strand of the target nucleic acid sequence and prepares the synthesis of the complementary DNA strand), and (i) the target nucleic acid sequence contained within the template sequence A template-dependent polymerization agent under conditions allowing a PCR cycling step comprising: annealing a primer necessary for amplification; and (ii) extending the primer (nucleic acid polymerase synthesizes a primer extension product) Amplifying a nucleic acid template sequence using a nucleic acid polymerase asA “a set of polynucleotide primers” or “a set of PCR primers” can include 2, 3, 4 or more primers.

  Other amplification methods include, but are not limited to, ligase chain reaction (LCR), polynucleotide specific base amplification (NSBA), or other methods known in the art.

  As used herein, the term “polynucleotide primer” refers to conditions under which synthesis of a primer extension product complementary to a nucleic acid template is catalyzed to produce a primer extension product complementary to the target nucleic acid template. Below is meant a DNA or RNA molecule that can hybridize to a nucleic acid template and serve as a substrate for enzymatic synthesis. The conditions for initiation and extension are four different in appropriate buffers ("buffers" include cofactors or substitutes that affect pH, ionic strength, etc.). This includes the presence of deoxyribonucleoside triphosphates and polymerization inducers such as DNA polymerase or reverse transcriptase, and appropriate temperatures. The primer is preferably single stranded for maximum efficiency in amplification. “Primers” useful in the present invention are generally about 10-35 nucleotides in length, preferably about 15-30 nucleotides in length, and most preferably about 18-25 nucleotides in length.

  A “tumor” as defined herein is a tumor that may be either malignant or non-malignant. Tumors of the same tissue type originate from the same tissue and can be classified into various subtypes based on their biological characteristics.

  The term “cancer” as used herein refers to a malignant disease caused by or characterized by the growth of cells that have lost their sensitivity to normal growth control. “Malignant disease” means a disease induced by a cell that has acquired the ability to invade the source tissue or be removed from the source tissue and migrate to a distant site.

  The term “antibody” as used herein means an immunoglobulin that has the ability to specifically bind to a given antigen. As used herein, the term “antibody” refers to any antibody of any isotype (IgG, IgA, IgM, IgE, etc.) and also specifically reactive to vertebrate proteins such as mammals. It is intended to include some of those fragments. Antibodies can be fragmented using conventional techniques, and the fragments can be screened for utility in the same manner as whole antibodies. Thus, this term includes segments of antibody molecules that are selectively cleaved with a given protein, cleaved by proteolysis or recombined portions. Non-limiting examples of such proteolytic and / or recombinant fragments include Fab, F (ab ′) 2 containing V [L] and / or V [H] domains joined by a peptide linker. , Fab, Fv, and single chain antibodies (scFv). The scFv can be linked covalently or non-covalently to form an antibody having two or more binding sites. The antibody can be labeled with a detectable moiety by those skilled in the art. In some embodiments, the antibody that binds to the entity desired to be measured (primary antibody) is not labeled, but instead is detected by the specific binding of the labeled secondary antibody to the primary antibody. .

  A patient may be treated if the one or more symptoms of the cancer described herein are eliminated or the severity is reduced or further progression or development is prevented. “Treated” by the invention.

  As used herein, the term “therapeutically effective amount” refers to the benefit of an important patient, ie treatment, cure, prevention or amelioration of the associated medical condition, or the therapeutic rate, cure rate of the condition. Means the total amount of each active ingredient of a pharmaceutical composition or method that is sufficient to show an increase in the prevention or improvement rate.

  The term “cancer therapeutic” as used herein refers to a compound that prevents the onset or progression of cancer, or prevents cancer metastasis, or reduces, delays or eliminates the symptoms of cancer. Means.

  The term “inhibitor of the mono-ubiquitination” as used herein refers to a compound that prevents or inhibits ubiquitination of the FANCD2 gene. “Ubiquitination” is defined as the covalent binding of ubiquitin to a protein by an E3 monoubiquitin ligase. In one preferred embodiment, “inhibitor of monoubiquitination” means any inhibitor of a FANC protein complex with E3FANCD2 monoubiquitin ligase activity, such that FANCD2 monoubiquitin ligase activity is inhibited.

As used herein, the term “cisplatin” means a substance with the following chemical structure:

Cisplatin, also called cis-diamine dichloroplatinum (II), is one of the most frequently used anticancer agents. Cisplatin is an active ingredient in several different drug combination therapy protocols used to treat a variety of solid tumors. These drugs are used to treat testicular cancer (using bleomycin and vinblastine), bladder cancer, head and neck cancer (using bleomycin and fluorouracil), ovarian cancer (using cyclophosphamide or doxorubicin) and lung cancer (etoposide) Is done. Cisplatin has been found to be the most active single agent against the majority of these tumors. Cisplatin is commercially available as “Platinol” from Bristol Myers Squibb. Cisplatin is one of many platinum coordination complexes with antitumor activity. Platinum compounds are DNA cross-linking agents that are similar but not identical to alkylating agents. Platinum compounds replace chloride ions with various types of nucleophilic groups. Both the cis and trans isomers do this, but the trans isomer is known to be biologically inactive for reasons that are not fully understood. In order to have antitumor activity, the platinum compound must have two relatively unstable cis-oriented leaving groups. The main reaction site is the N7 atom of guanine and adenine. The main interaction is the formation of interchain bridges between the drug and adjacent guanine. Interchain crosslinking has been shown to correlate with clinical response to cisplatin therapy. DNA / protein cross-linking also occurs, but this does not correlate with cytotoxicity. No cross-resistance between the two drug groups is usually seen, indicating that the mechanism of action is not identical. The type of crosslinking with DNA can differ between platinum compounds and typical alkylating agents.

  As used herein, “resistance to one or more anti-neoplastic agents” refers to the ability of a cancer cell to develop resistance to an anti-cancer agent. The mechanism of drug resistance includes decreased intracellular drug levels caused by increased drug efflux or decreased inward transport, increased drug inactivation, decreased conversion of the drug to the active form, target enzyme or Includes changes in receptor quantity (gene amplification), reduced affinity of target enzyme or receptor for drug, enhanced repair of drug-induced defects, reduced enzyme activity required for killing (topoisomerase II) . In a preferred embodiment of the present invention, drug resistance means enhanced repair of DNA damage induced by one or more anti-tumor agents. In another preferred embodiment of the invention, the enhanced repair of DNA damage induced by one or more anti-tumor agents is by a constitutively active Fanconi anemia / BRCA DNA repair pathway.

  The term “anti-neoplastic agent” as used herein means a compound used to treat cancer. According to the present invention, “anti-tumor agents” include chemotherapeutic compounds as well as other anti-cancer agents known in the art. In a preferred embodiment, the “antitumor agent” is cisplatin. Anti-tumor agents according to the present invention also include cancer therapy protocols that use chemotherapeutic compounds in conjunction with radiation therapy and / or surgery. Radiation therapy relies on the local destruction of cancer cells by ionizing radiation that disrupts cellular DNA. Radiation therapy can be initiated externally or from within the body at high or low doses and can be delivered to the tumor site with computer-assisted accuracy. Brachytherapy, or intra-tissue radiation therapy, can place the radiation source directly into the tumor as implanted “seeds”.

  As used herein, the term “a reduced growth rate” refers to a tumor cell line that has not been treated with a potential inhibitor of the Fanconi anemia / BRCA pathway and one or more chemotherapeutic compounds. 50%, preferably 90%, more preferably in cell growth rate of tumor cell lines being treated with potential inhibitors of Fanconi anemia / BRCA pathway and one or more chemotherapeutic compounds compared to cells A reduction of 99% and most preferably 100% is meant.

  As used herein, the term “chemosensitizing agent” sensitizes a cell or population of cells to a chemotherapeutic compound and produces a “reduced growth rate” as defined herein. Any compound is meant. Chemosensitizers are compounds that are generally not cytotoxic per se but modify host cells or tumor cells to enhance anticancer therapy. According to the present invention, cellular resistance to chemotherapeutic compounds is reversed in the presence of chemosensitizers. In certain preferred embodiments, the chemosensitizer is an inhibitor of the Fanconi anemia / BRCA pathway. In the most preferred embodiment, the chemosensitizer is an inhibitor of monoubiquitination of the FANCD2 protein.

  As used herein, “methylation status of Fanconi anemia / BRCA pathway gene” refers to one or more methylated cytosines in the Fanconi anemia / BRCA pathway gene (5 m−). Associated with the presence of C), resulting in a 90%, 99% or preferably 100% reduction or inhibition of gene expression compared to the unmethylated gene. In a preferred embodiment, the methylated cytosine is present within the CpG island. According to the present invention, a gene is said to be “methylated” when one or more CpG residues are methylated.

  As used herein, “microarray” or “array” means a number of unique biomolecules attached to one surface of a solid support. Preferably, the biomolecules of the present invention are potential inhibitors of the Fanconi anemia / BRCA pathway described herein. In this embodiment, the microarray of the invention comprises nucleic acids, proteins, polypeptides, peptides, fusion proteins or small molecules immobilized on a solid support, generally at a high density. Each biomolecule is attached to the surface of a solid support in a preselected region. Suitable solid supports are commercially available and will be apparent to those skilled in the art. These supports can be made from materials such as glass, ceramic, silica and silicon. The support typically comprises a flat (planar) surface, or at least an array in which the molecules to be examined are coplanar. In one embodiment, the array is on microbeads. In one embodiment, the array comprises at least 10, 500, 1,000, 10,000 different biomolecules attached to one surface of a solid support.

Detailed Description “FANCD2-L therapeutic agent” means any protein isoform, including peptides, peptide derivatives, analogs or isomers of FANCD2-L protein, and FANCD2- Further included are any small molecule derivatives, analogs, isomers or agonists that are functionally equivalent to L. Also included in this definition is a gene-activated nucleic acid or nucleic acid that may be a full-length or partial-length gene sequence or cDNA, or that contains an aptamer of an antisense molecule that can act to regulate gene expression A nucleic acid encoding FANCD2, which may be a binding molecule.

  “Nucleic acid encoding FANCD-2” includes the complete cDNA or genomic sequence of FANCD2 or a portion thereof for expressing FANCD2-L protein, as defined above. Nucleic acids may be further contained within a nucleic acid carrier or vector and include nucleic acids that are appropriately modified for effective delivery to a target site.

  “Stringent conditions of hybridization” generally includes temperatures above 30 ° C., typically above 37 ° C., preferably above 45 ° C. Stringent salt conditions are usually less than 1,000 mM, typically less than 500 mM, and preferably less than 200 mM.

  “Substantially homology or similarity” with respect to a nucleic acid means that the nucleic acid or fragment thereof is “substantially homologous” to another nucleic acid or fragment thereof (or “substantially similar”). At least about 60% of the nucleotide bases when optimally aligned (including appropriate nucleotide insertions or deletions) with other nucleic acids (or their complementary strands), Usually refers to nucleotide sequence identity at least about 70%, more usually at least about 80%.

  “Antibodies” includes polyclonal and / or monoclonal antibodies and fragments thereof, including single chain antibodies and Fab fragments, and their immunology with sufficient binding specificity to identify protein isoforms. The static coupling equivalent is included. These antibodies will be useful in assays as well as pharmaceuticals.

  “Isolated” is used to describe a protein, polypeptide, or nucleic acid that is separated from components that naturally accompany it. An “isolated” protein or nucleic acid is substantially pure if at least about 60-75% of the sample exhibits a single amino acid or nucleotide sequence.

  “Regulatory sequences” means sequences that are usually within the 100 kb coding region of a locus, but they also express gene expression (transcription of genes, and translation, splicing, stabilization of messenger RNA) It may be further away from the coding region that affects the

  “Polynucleotide” includes both sense and antisense strand RNA, cDNA, genomic DNA, synthetic, and mixed polymers and, as will be readily appreciated by those skilled in the art, chemical Or it may be biochemically modified or may contain non-natural or derivatized nucleotide bases. Such modifications include, for example, labeling, methylation, substitution with one or more analogs of natural nucleotides, uncharged chains (eg, methyl phosphonate, phosphotriester, phosphoamidate, carbamate, etc.) and charge. Internucleotide modifications such as linkages (eg, phosphorothioate, phosphorodithioate, etc.), pendant moieties (eg, polypeptides), and modified linkages (eg, alpha anomeric nucleic acids, etc.) are included. Similarly, synthetic molecules that mimic nucleic acids in their ability to bind to specified sequences via hydrogen bonding and other chemical interactions are also included.

  A “mutation” is a change in a nucleotide sequence within or outside of a regulatory sequence compared to the wild type. A change is a deletion, substitution, which makes a difference between the nucleic acid or protein sequence of a gene that is normally expressed in a functional cell and the nucleic acid or protein sequence when expression and functionality are in the normal range. It may be in the form of point mutations, multiple nucleotide mutations, transpositions, inversions, frameshift mutations, nonsense mutations, or other abnormalities.

  “Subject” means an animal, including mammals, including humans.

  By “wild type FANCD2” is meant a gene that encodes a protein or expressed protein that can be monoubiquitinated to produce FANCD2-L from FANCD-S in a cell.

  The inventors have found that some Fanconi anemias are telangiectasia ataxia (AT), xeroderma pigmentosum (XP), Cocaine syndrome (CS), Bloom syndrome, myelodysplastic syndrome, aplastic anemia. We found similarities with a group of syndromes, including cancer susceptibility syndrome and HNPCC (hereditary nonpolyposis colorectal cancer) (see Table 2). These syndromes have fundamental defects in DNA repair and are associated with defects in maintaining chromosomal integrity. Defects in pathways associated with DNA repair and maintenance of chromosomal integrity cause genomic instability and cellular sensitivity to DNA damaging agents such as bifunctional alkylating agents that induce interstrand cross-linking. Furthermore, defects in the DNA repair machinery appear to substantially increase the probability of initiating a range of cancers by gene rearrangement. This observation is valid for clinical use of DNA cross-linking drugs, including mitomycin C, cisplatin, cyclophosphamide, psoralen and UVA radiation.

Fanconi anemia is a rare disease, but the multi-phenotypic effects of FA are wild-type of FA protein in pathways for various cellular processes, including genome stability, apoptosis, cell cycle control and resistance to DNA cross-linking It represents the importance of the function. The cell abnormalities in FA, susceptibility to crosslinking agents, extension of the G2 phase of the cell cycle; poor growth at ambient O _2, overproduction of O ₂ radical, insufficient O ₂ radical defense, loss of superoxide dismutase Sensitivity to ionizing radiation (G2 phase specific); tumor necrosis factor overproduction, direct defects in DNA repair including accumulation of DNA adducts, and defects in repair of DNA bridges, spontaneous Includes genomic instability, including chromosomal breakage, and hypermutability due to deletion mechanisms, increased apoptosis, defective p53 induction, endogenous stem cell defects including reduced colony growth in vitro; and decreased gonadal stem cell survival .

  These features reflect the involvement of FA in the maintenance of hematopoietic and gonadal stem cells and in the development of normal embryos in a number of different structures, including the skeletal and genitourinary systems. Patient-derived cell samples were analyzed to determine defects in the FA-D complementation group. Lymphoblasts from one patient produced the PD20 cell line, which may be mutated in a different gene from HSC62 from another patient with a defect in the D complementation group. I found it. Since the mutations from both patients were mapped to different genes in the D complementation group, two FANCD protein names—FANCD1 (HSC62) and FANCD2 (PD20) were generated (Timers et al., (2001)). Molecular Cell, vol. 7, p241-248). We have found that FANCD2 is the endpoint of the FA pathway, is not part of the FA nuclear complex, and is not required for its assembly or stability, and FANCD2 is FANCD2-S and FANCD2 It was shown to exist in two isoforms of -L. The inventors have also shown that transformation from a short chain protein (FANCD2-S) to a long chain protein (FANCD2-L) occurs in response to the FA complex (FIG. 8). Defects in specific proteins associated with the FA pathway result in failure to create important post-translationally modified forms of FANCD2 identified as FANCD2-L. Two isoforms of FANCD2 have been identified as short and long chain forms.

  Failure to create FANCD2-L correlates with errors in DNA repair and cell cycle abnormalities associated with the diseases listed above.

  To understand in more detail the role of FANCD2 in the above mentioned syndromes, we cloned the FANCD2 gene and determined the protein sequence. The FANCD2 gene has an open reading frame of 4,353 base pairs and 44 exons encoding a novel 1,451 amino acid nucleoprotein with a predicted molecular weight of 166 kD. Western blot analysis revealed the presence of two protein isoforms, 162 and 155 kD. The sequences corresponding to the 44 intron / exon junction are shown in Table 6 (SEQ ID NOs: 9-94).

  Unlike previously cloned FA proteins, FANCD2 proteins from several invertebrate eukaryotic cells are Melanogaster (Drosophila melanogaster), A. Taliana (Arabidopsis thaliana), and C.I. It showed a highly significant alignment score with the protein in elegance. Drosophila homologs have 28% amino acid identity and 50% similarity to FANCD2 (Figure and SEQ ID NO: 1-3), but no functional studies have been performed in each species. E. coli or S. coli. In cerevisiae, no protein similar to FANCD2 was found.

  We obtained the FANCD2 DNA sequence (SEQ ID NO: 5) by analyzing the chromosomal 3P locus in PD20 and VU008, but the two FA cell lines have biallelic mutations in the FANCD2 gene (FIG. 10). These cell lines were designated as D complementation group because patient-derived lymphoblasts could not complement HSC62, which is the reference cell line for group D. No FANCD2 mutation was detected in this D group reference cell line, indicating that the gene mutated in HSC62 is a gene encoding FANCD1, and in PD20 and VU008 it is FANCD2 (FIG. 11). To identify mutations, a microcell-mediated chromosomal transfer method was used (Whitney et al., Blood, (1995), vol. 88, p49-58). Detailed analysis of five microcell hybrids containing small overlapping deletions including loci narrowed the candidate region of the FANCD2 gene to 200 kb. The FANCD2 gene was isolated as follows: Three candidate ESTs were located in or near this FANCD2 critical region. Genes were sequenced using 5 'and 3' RACE to obtain full-length cDNAs, and each expression pattern was analyzed by Northern blotting. EST SCC34603 had a ubiquitous and low level expression of 5 kb and 7 kb mRNA similar to the previously cloned FA gene. Open reading frames for TIGR-A004X28, AA609512 and SGC34603 were found and the lengths were 234,531 and 4413 bp, respectively. All three were analyzed for mutations in PD20 cells by sequencing the cloned RT-PCR product. No sequence changes were detected in TIGR-A004X28 and AA609512, but 5 sequence changes were found in SGC34603. Next, we determined the structure of the SGC34603 gene by using cDNA sequencing primers on BAC 177N7 from the critical region.

  Based on genomic sequence information, PCR primer pairs are designed (Table 7), allons containing the putative mutations are amplified, and allele-specific assays are developed to screen the PD20 family as well as the 568 control chromosome did. The three alleles were common polymorphisms; however, no two changes were found in the controls, thus indicating a potential mutation (Table 3). The first was a maternally inherited A → G change at nt376. In addition to changing the amino acid (S126G), this change was associated with mis-splicing and insertion of 13 bp from intron 5 into the mRNA. 43/43 (100%) independently cloned RT-PCR products containing maternal mutations contained this insert, but only 3% (1/31) in the control cDNA clone were misspliced. mRNA was shown. The 13 bp insertion produces a frameshift, predicting a severely short protein of only 180 amino acids in length. The second change was a paternal genetic missense change at position 1236 (R1236H). Isolation of mutations in the PD20 core family is shown in FIG. Since the SGC34603 gene of PD20 contains both maternal and paternal alleles that are not present on the 568 control chromosome, and the maternal mutation was associated with mis-splicing in 100% of the analyzed cDNA, Concluded that SGC34603 is a FANCD2 gene.

  The protein encoded by FANCD2 is absent in PD20: To further confirm the identity of SGC34603 as FANCD2, antibodies were raised against the protein and Western blot analysis was performed (FIG. 11). . Antibody specificity was demonstrated by retroviral transduction and stable expression of FANCD2 in PD20 cells (FIG. 11). In wild type cells, this antibody detected two bands (155 and 162 kD) that we called FANCD2-S and -L (most obvious in FIG. 11). FANCD2 protein levels were significantly reduced in all MMC sensitive cell lines from patient PD20 (FIG. 11a, lanes 2, 4), but were present in FA cells from wild type cell lines and other complementation groups. . Furthermore, PD20 cells corrected by microcell-mediated introduction of chromosome 3 also produced normal amounts of protein (FIG. 11a, lane 3).

  Functional complementation of FA-D2 cells with FANCD2 cDNA: We next evaluated the ability of the cloned FANCD2 cDNA to complement the MMC sensitivity of FA-D2 cells (FIG. 12). Full length FANCD2 cDNA was subcloned into the retroviral expression vector pMMP-puro as previously described (Pulsipher et al., (1998), Mol. Med., Vol. 4, p468-479). Transduced PD-20 cells expressed FANCD2-S and FANCD2-L, both isoforms of FANCD2 protein (FIG. 12c). Transduction of PA-D2 (PD20) cells with pMMP-FANCD2 corrected the MMC sensitivity of the cells. These results further demonstrate that the cloned FANCD2 cDNA encodes a FANCD2-S protein that can be post-translationally modified to a FANCD2-L isoform. This important modification is discussed in more detail below.

  Analysis of phenotypic backmutated PD20 clones: We next generated additional evidence demonstrating that sequence changes in PD20 cells are not functionally neutral polymorphisms. For this purpose, we performed a molecular analysis of a revertant lymphoblast clone (PD20-cl.1) from patient PD20, which is no longer sensitive to MMC. Phenotypic backmutation and somatic mosaicism are frequent findings in FA and have been associated with intragenic events such as mitotic recombination or compensatory frameshifts. Indeed, ˜60% of maternally derived SGC34603 cDNA had a novel splice variant that inserts a 36 bp intron 5 sequence rather than the 13 bp normally observed (FIG. 13). The occurrence of this in-frame splice variant correlated with a new base change from G to A at position IVS5 + 6, and correct reading frame recovery was confirmed by Western blot analysis. In contrast to all MMC sensitive fibroblasts and lymphoblasts from patient PD20, PD20-cl. 1 produced an easily detectable amount of FANCD2 protein with a slightly higher molecular weight than the normal protein.

  Analysis of cell lines from other “FANCD” patients: antibodies are also the reference cell line for the FA-D group, HSC, and two other cell lines identified as group D by the European Fanconi Anemia Registry (EUFAR) Were used to screen additional FA patient cell lines. VU008 did not express FANCD2 protein, both were found to be heterozygotes for the compound, including missense and nonsense mutations in exon 12, but not found on the 370 control chromosome (Table 3, FIG. 11). The missense mutation appears to destabilize the FANCD2 protein because it cannot be detected in lysates from VU008 cells. PD733 from the third patient also lacked the FANCD2 protein (FIG. 11b, lane 3), and splice mutations were found that led to the absence of exon 17 and an internal deletion of the protein. The correlation between the mutation and the lack of FANCD2 protein in cell lysates from these patients demonstrates the identity of FANCD2 with the FA gene. In contrast, in HSC62, easily detectable amounts of both isoforms of FANCD2 protein were found (FIG. 11a, lane 8), and VU423 cDNA and genomic DNA from both cell lines were found. The mutation was extensively analyzed but nothing was found. Furthermore, whole cell fusion between VU423 and PD20 fibroblasts showed complementation of the chromosomal breakage phenotype (Table 5). Taken together, these data demonstrate that the FA-D group is genetically heterogeneous and that the genes missing in HSC62 and VU423 are distinct from FANCD2.

  FANCD2 gene and protein identification and sequencing includes therapeutic drug development, diagnostic tests and screening assays for diseases associated with DNA repair deficiencies and cell cycle abnormalities, including but not limited to those listed in Table 2 Provides a new target for

  The following description provides new and useful insights regarding the biological role of FANCD2 in the FA pathway, which is the basis for diagnosing and treating the above syndromes.

  Evidence that FA cells have a fundamental molecular defect in cell cycle regulation includes: (a) FA cells have a 4N DNA content that is enhanced by treatment with chemical crosslinkers. (B) cell cycle arrest and decreased proliferation of FA cells can be partially corrected by overexpression of protein SPHAR, a member of the cyclin family of proteins; and (c) caffeine is FA Cancels G2 phase arrest of cells. Consistent with these results, caffeine constitutively activates cdc2 and may invalidate the normal G2 phase cell cycle checkpoint in FA cells. Finally, the FANCC protein binds to the cyclin-dependent kinase cdc2. We propose that the FA complex may be a substrate or regulator of the cyclin B / cdc2 complex.

  Furthermore, evidence that FA cells have a fundamental defect in DNA repair is (a) sensitive to DNA crosslinkers and ionizing radiation (IR), suggesting specific defects in cross-linked DNA repair or double-strand breaks. FA cells; (b) DNA damage in FA cells resulting in a highly active p53 response, suggesting that there is a defective but intact checkpoint activity; and (c) non-homologous end joining FA cells with defects in fitness and increased proportion of homologous recombination, (Garcia-Higuera et al., Mol. Cell., (2001), vol. 7, p249-262), (Grompe et al., Hum. Mol. Genet., (2001), vol. 10, p1-7).

  Despite these common abnormalities in cell cycle and DNA repair, the mechanism by which the FA pathway regulates these activities has been difficult to understand. We herein demonstrate that the FANCD2 protein functions downstream of the FA protein complex. In the presence of the assembled FA protein complex, FANCD2 protein is activated to a high molecular weight monoubiquitinated isoform that appears to modulate the S phase specific DNA repair reaction. Activated FANCD2 protein accumulates in the nuclear focus in response to DNA damaging agents and co-localizes and co-immunoprecipitates with the known DNA repair protein BRCA1. These results resolve the previous conflicting FA pathway model (D'Andrea et al., 1997) and indicate that FA proteins cooperate in cellular responses to DNA repair.

  The FA pathway involves the formation of an FA multi-subunit nuclear complex that also includes FANCF as a subunit of the complex in addition to the A / C / G proven by the inventors (FIG. 8). The FA pathway becomes “active” during S phase, producing an S phase specific repair or checkpoint response. Normal activation of the FA pathway, which is dependent on the FA multi-subunit complex, leads to a regulated monoubiquitination of phosphoprotein-FANCD2 into a high molecular weight activated isoform identified as FANCD-2L via a phosphorylation step. (Fig. 1). Monoubiquitination is associated with cell trafficking. FANCD2-L appears to regulate the S phase specific DNA repair reaction (FIG. 3). Failure to activate S phase specific activation of FANCD2 by FA cells is associated with cell cycle specific abnormalities. Activated FANCD2 protein accumulates in the nuclear focus in response to DNA damaging agents, MMC and IR and co-localizes and co-immunoprecipitates with the known DNA repair protein BRCA1 (FIGS. 4-6). These results resolve a conflicting model of previous FA protein function (D'Andrea et al., 1997) and strongly support the role played by the FA pathway in DNA repair.

  The inventors for the first time identified an association between FANCD2 isoforms involved in the FA pathway and proteins, which are known diagnostic molecules for various cancers. Similar pathways for DNA damage for BRCA1 protein activated to high molecular weight post-translationally modified isoforms in S phase or in response to DNA damage suggest that activated FANCD2 protein interacts with BRCA1 ing. More specifically, regulatory monoubiquitination of FANCD2 appears to target the FANCD2 protein target to a nuclear focus containing BRCA1. FANCD2 can co-immunoprecipitate with BRCA1 and further bind to other “dot” proteins such as RAD50, Mre11, NBS, or RAD51. Recent studies have demonstrated that the BRCA1 focus is composed of a large (2 megadalton) multiprotein complex (Wang et al., Genes Dev., (2001) vol. 14, p927-939). This complex includes ATM, an ATM substrate related to DNA repair function (BRCA1), and an ATM substrate related to checkpoint function (NBS). Furthermore, damage recognition and activation of the FA pathway has been suggested to involve kinases that respond to DNA damage, including ATM, ATR, CHK1, or CHK2.

  We have found that DNA damaging agents, IR and MMC activate independent post-translational modifications of FANCD2, resulting in distinct functional results. IR activates ATM-dependent phosphorylation of FANCD2 at serine 222 to produce an S phase checkpoint reaction. MMC activates BRACA-1-dependent and FA pathway-dependent monoubiquitination of FANCD2 at lysine 561, resulting in FANCD2 / BRCA1 nuclear focus assembly and MMC resistance. Thus, FANCD2 has two independent functions in maintaining chromosomal stability resulting from two separate post-translational modifications that provide a link between two additional cancer susceptibility genes (ATM and BRCA1) within a common pathway. Have a social role. Some additional evidence supports the interaction between FANCD2 and BRCA1. First, the BRCA1 (− / −) cell line, HCC 1937 (Scully et al., Mol. Cell, (1999), vol. 4, p1093-1099), has increased chromosomal instability and triradiation and tetraradiation chromosome formation. Along with the "Fanconi anemia-like" phenotype. Second, FA cells usually form a BRCA1 focus (and RAD51 focus) in response to IR, but BRCA1 (− / −) cells do not have a detectable BRCA1 focus and are compared to normal cells. As a result, the number of FANCD2 focuses is greatly reduced. Functional complementation of BRCA1 (− / −) cells restored BRCA1 focus and FANCD2 focus to normal levels and restored normal MMC resistance.

  The amount of FANCD2-L depends in part on the amount of FAND2-S synthesized from the fancd2 gene, and in part, the use of the FA complex to monoubiquitinated FANCD2-S to form FANCD2-L Determined by possibility. Determining the association of FANCD2-L with nuclear focus, including BRCA and ATM, and the role of FANCD2-L in DNA repair is a powerful tool to consider potential cancer development in patients for a wide range of cancers To the right target. Such cancers include cancers that arise due to damage on chromosome 3p, as well as cancers on other chromosomes where the mutation results in disruption of production of upstream members of the FA pathway, such as FANCG, FANCC, or FANCA. Is included. Primary cells from cancer patients, including cancer cell lines and tumor biopsy tissues, have been screened for FANCD-L and abnormal levels of this protein are expected to correlate with early diagnosis of the disease. Since FANCD2 protein is the final step in the pathway to DNA repair, any abnormalities in the protein in one or more pathways that cause the conversion of FANCD2-S to FANCD-L are easily detected by measuring FANCD2 levels. It is thought. In addition, the level of FANCD2 affects how other proteins such as BRCA and ATM interact functionally in the nucleus, with serious consequences for patients. Analysis of the level of FANCD2 in a patient is expected to help physicians make clinical decisions regarding the understanding of the class of cancer that the patient exhibits. For example, if a cancer cell is unable to produce a monoubiquitinated FANCD2-L isoform, the cell has increased chromosomal instability and may have increased sensitivity to radiation or chemotherapeutic drugs . This information will help doctors improve patient care.

  Fanconi anemia is associated not only with a wide spectrum of various cancers but also with congenital abnormalities. Fetal development is a complex but orderly process. Certain proteins have a particularly broad spectrum of effects, as they disrupt this orderly developmental progression. The FA pathway plays a critical role in the development and disruption of the FA pathway and causes numerous adverse effects. Errors in the FA pathway can be detected through analysis of FAND2-L protein from fetal cells. FANCD2 is a diagnostic marker for normal fetal development and a potential target for therapeutic intervention.

  Consistent with the above, the inventors have demonstrated that FANCD2 plays a role in the production of viable sperm. FANCD2 forms a focus on the unpaired axis of the XY bivalent chromosome in late mitotic and multifilament mouse spermatocytes (FIG. 7). Interestingly, FANCD2 focus is also seen in autosomal telomeres at the doublet stage. Considered in conjunction with known deficits in fertility in FA patients and FA-C knockout mice, our observations are active for normal development of spermatocytes throughout meiosis I This suggests that a modified FANCD2 protein is required. Most of the FANCD2 focus found on the XY axis has been found to co-localize with the BRCA1 focus, suggesting that the two proteins function together in meiotic cells. Similar to BRCA1, FANCD2 was detected on the axial (unsynapted) element of the developing synaptonemal structure. Since recombination occurs in the synaptic region, FANCD2 can function before recombination is initiated, possibly to help prepare the chromosome for synapsis or to regulate subsequent recombination events. . A relatively synchronous method whereby FANCD2 assembles on meiotic chromosomes and forms dot structures in meiotic cells, FANCD2 plays a role in cell cycle control during both mitosis and meiosis Suggests that.

  Embodiments of the present invention are directed to the use of FANCD-2L, a post-translationally modified isoform, as a diagnostic target to determine FA pathway integrity. FANCD2 ubiquitination and FANCD2 intranuclear focus formation are downstream events in the FA pathway and require the function of several FA genes. The inventors have found that biallelic mutations in any of the upstream FA genes (FANCA, FANCB, FANCC, FANCE, FANCF and FANCG) are caused by non-ubiquitinated FANCD2 (FANCD2-S) type to ubiquitinated FANCD2 (FANCD2-). L) found to block post-translational modification of FANCD2 to form. Any of these upstream defects can be reversed by transfecting the cells with FANCD2 cDNA (FIG. 1a).

  We have demonstrated for the first time the presence of FANCD2 and its role in the FA pathway. We have demonstrated that when FANCD2 is associated with other DNA repair proteins such as BRCA1 and ATM, FANCD2 accumulates in the nuclear focus in response to DNA damaging agents. We also note that FANCD2 exists in cells in two isoforms, and a decrease in FANCD2-L, one of these two isoforms, correlates with increased Fanconi anemia and cancer susceptibility. certified. We have used these findings to propose a number of diagnostic tests for clinical use to help patient care.

  These tests include: (a) Genetic and prenatal counseling for future offspring or parents concerned about hereditary Fanconi anemia in the current pregnancy; (b) Cancer susceptibility correlated with a defective FA pathway Genetic counseling and immunodiagnostic testing for human adults to determine the increase; and (c) to provide an opportunity to develop a treatment protocol that is most effective for the subject with minimal side effects Diagnosing cancer already present in the subject.

  The diagnostic tests described here are based on standard protocols known in the art, so we have provided new reagents for testing for FANCD2 protein and nucleotide sequences. These reagents include antibodies specific for FANCD2 isoforms, nucleotide sequences from which vectors, probes and primers are derived to detect genetic changes within the FANCD2 gene, and to preserve and examine defects in the FA pathway. Cell lines and recombinant cells.

  We prepared monoclonal and polyclonal antibody preparations described in Example 1 that are specific for FANCD2-L and FANCD2-S proteins. In addition, FANCD2 isoform-specific antibody fragments and single chain antibodies can be prepared using standard techniques. We used these antibodies in wet chemical assays, such as immunoprecipitation assays such as Western blotting, to identify FANCD2 isoforms in biological samples (Figure 1). Conventional immunoassays can also be used, including enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), immunoradiometric assay (IRMA) and immunoenzyme assay (IEMA), and further including sandwich assays. Other immunoassays can utilize samples of whole cells or lysed cells that are reacted with antibodies in solution and optionally analyzed in liquid form in a reservoir. FANCD2 isoforms are detected in intact cells, including cell lines, biopsy tissues and blood, by immunological techniques using, for example, fluorescence activated cell sorting and laser or light microscopy to detect immunofluorescent cells. It can be identified in situ (FIGS. 1-7, 9-14). For example, a biopsy tissue or cell monolayer embedded in paraffin or prepared on a slide in a preserved state, such as a frozen tissue section, is exposed to an antibody to detect FANCD2-L, and then It can be examined with a fluorescence microscope.

  In an embodiment of the present invention, immunoblotting and immunofluorescence methods are used to provide a new simple diagnostic test for patient-derived cell lines or cancer cell lines to detect changes in the amount of FANCD2 isoforms. Analyzed by law. Diagnostic tests also provide a means to screen for upstream defects in the FA pathway and a practical alternative to the DEB / MMC chromosomal breakage test for currently used FA, which is upstream in the FA pathway This is because individuals with certain deficiencies cannot ubiquitinate FANCD2. Retroviral gene transfer to form transformed patient-derived cell lines to provide rapid subtype analysis of patients newly diagnosed with any of the syndromes listed in Table 2, particularly FA. Other assays can be used, including assays combined with FANCD2 immunoblotting (Pulsipher et al., Mol. Med., (1998) vol. 4, p468-79).

  The above assay can be performed by a diagnostic laboratory or a diagnostic kit can be manufactured and sold to health care providers or individuals for self-diagnosis. The information obtained from the results of these tests and their interpretation is useful for health care providers in diagnosing and treating a patient's condition.

  Genetic testing can provide a quick and reliable risk analysis for a particular condition for a subject compared to an epidemiological baseline. Our data suggest that genetic heterogeneity occurs in patients with FA within the FANCD2 complementation group. The inventors have found a correlation between genetic heterogeneity and disease, and between genetic heterogeneity and abnormal post-translational modifications that result in the presence or absence of FANCD2-L. This correlation provides the basis for prognostic testing and diagnostic testing and treatment for any of the syndromes characterized by abnormal DNA repair. For example, nucleic acid from a cell sample obtained from blood collection or from other cells from the subject can be analyzed for mutations in the FANCD2 gene and the subject can be diagnosed as having increased susceptibility to cancer.

  The present inventors confirmed the localization of the FANCD2 gene at 3p25.3 on chromosome 3p in a region correlated with high frequency of cancer. Cytogenetic and loss of heterozygosity (LOH) studies have demonstrated that deletion of chromosome 3p occurs frequently in all forms of lung cancer (Todd et al., Cancer Res., Vol. 57). , P 1344-52). For example, homozygous deletions were found in 3 squamous cell lines within the 3p21 region. Homozygous deletions were also found at 3p12 and 3p14.2 in small cell carcinomas (Franklin et al., Cancer Res. (1997), vol. 57, p 1344-52). The mapping of FANCD2 in the present invention supports the theory that this chromosomal region contains an important tumor suppressor gene. Another support for this is the recent publication of Sekine et al., Human Molecular Genetics, (2001), which reports the localization of a novel susceptibility gene for familial ovarian cancer to chromosome 3p22-p25. vol. 10, p 1421-1429. The reduction or lack of FANCD2-L is not limited to the FANCD2 site (3p25.3) herein, but also from defects in DNA repair after cell damage resulting from exposure to environmental agents and normal aging processes. It has been proposed to be diagnostic about the increased risk of tumors that occur as a result of mutations, possibly also in other parts of the chromosome that occur.

  As more individuals and families are screened for genetic defects in the FANCD2 gene, a database is developed that collects population frequencies for various mutations and continues to improve the predictive value of genetic analysis. There will be a correlation between these mutations and the health profile for the individual. An example of an allele-specific family analysis for FANCD2 is provided for two families in FIG.

  Diagnosis of a mutation in the FANCD2 gene can be detected initially by a rapid immunological assay to detect a decrease in the amount of FANCD2-L protein. Positive samples can then be screened using available probes and primers for defects in any gene in the PA pathway. If a defect in the FANCD2 gene is involved, mutations can be detected using primers or probes as shown in Table 7. Within those samples, if no mutation is detected by such a primer or probe, the entire FANCD2 gene can be sequenced to determine the presence and location of the mutation within the gene.

  Nucleic acid screening assays used to identify genetic defects at the FANCD2 locus can include PCR-type and non-PCR-type assays for detecting mutations. There are a number of approaches to analyze the cellular genome for the presence of mutations within a particular allele. For example, wild type FANCD2 allele changes, whether point mutations, deletions or insertions, can be detected using standard methods using probes (US Pat. No. 6,033,857). . Standard methods include: (a) Fluorescent in situ hybridization (FISH) that can be used on whole intact cells; and (b) detecting mutations using hybridization techniques on isolated nucleic acids. Allele-specific oligonucleotides (ASO) that can be used are included (Conner et al., Hum. Genet., (1989), vol. 85, p55-74). Other techniques include (a) a method of observing changes in the electrophoretic mobility of single-stranded DNA on a non-denaturing polyacrylamide gel, and (b) hybridizing a FANCD2 gene probe to genomic DNA isolated from a tissue sample. A method, (c) a method of hybridizing an allele-specific probe to genomic DNA of a tissue sample, (d) amplifying all or part of the FANCD2 gene from the tissue sample to produce an amplified sequence, A method for sequencing, (e) a method for amplifying all or part of the FANCD2 gene from a tissue sample using primers for a specific FANCD2 mutant allele, (f) for creating a cloned sequence Molecular cloning of all or part of the FANCD2 gene derived from tissue samples A method of sequencing a cloned sequence, (g) mismatch between a (i) FANCD2 gene or FANCD2 mRNA isolated from a tissue sample and (ii) a nucleic acid probe complementary to a human wild type FANCD2 gene sequence, A method of identifying when molecules (i) and (ii) are hybridized to each other to form a duplex, (h) amplification of a FANCD2 gene sequence in a tissue sample, and wild type FANCD2 gene sequence Hybridization of amplified sequence to nucleic acid probe, (i) Amplification of FANCD2 gene sequence in tissue sample, and Hybridization of amplified sequence to nucleic acid probe containing mutant FANCD2 gene sequence, (j) Deletion mutation in tissue sample Screening for (k) in tissue samples Screening for point mutations, (l) screening for insertional mutations in tissue samples, and (m) in situ hybridization of FANCD2 genes in tissue samples using nucleic acid probes containing FANCD2 genes. .

  For point mutations, it is often desirable to examine a relatively short region of a gene or genome: the large number of oligonucleotides required to examine all potential sites within a sequence is an efficient combinatorial method (Southern, EM et al., Nucleic Acids Res., (1994) vol. 22, pp. 1368 to 1373). Arrays can be used in combination with ligases or polymerases to search for mutations at all sites in the target sequence (US Pat. No. 6,307,039). Analysis of mutations by hybridization can be performed, for example, by gel, array, or dot blot.

  All genes can be sequenced to identify mutations (US Pat. No. 6,033,857). Sequencing of the FANCD2 locus can be accomplished using an oligonucleotide tag from a minimal cross-hybridizing set that attaches to complement on a solid support when attached to a target sequence (US Pat. No. 6 , 280, 935).

  Other methods for detecting mutations in the FANCD2 gene were described in US Pat. No. 6,297,010, US Pat. No. 6,287,772 and US Pat. No. 6,300,076. Methods are included. It is further envisaged that analysis of multiple samples using nucleic acid microchip technology or lab-on-chip can be used in these assays. Subsequently, using the correlation of these mutations with the results of genetic studies on breast cancer, ovarian cancer or prostate cancer patients, whether the defects identified in the FANCD2 gene are cancer-related defects according to the present invention Can be determined.

  Subjects who have developed a tumor can be screened using nucleic acid diagnostic tests or antibody-based tests to detect FANCD2 gene mutations or deficiencies in the FANCD2-L protein. Based on such screening, the samples are melanoma, leukemia, astrocytoma, glioblastoma, lymphoma, glioma, Hodgkin lymphoma, chronic lymphocytic leukemia and pancreatic cancer, breast cancer, thyroid cancer, ovarian cancer, uterus Available from patients with a wide range of cancers including cancer, testicular cancer, pituitary cancer, kidney cancer, gastric cancer, esophageal cancer and rectal cancer. The clinician has an improved ability to select an appropriate treatment protocol to maximize treatment benefit for the patient. In particular, the presence of genetic damage or deficiencies in the FANCD2-L protein can be correlated with responsiveness to various current chemotherapeutic drugs and radiation therapy.

  New therapies may be developed by screening molecules that modulate FANCD2-S monoubiquitination that produces FANCD2-L in cellular assays (Examples 11-12) and knockout mouse models (Example 10). it can. Such molecules include molecules that bind directly to molecules such as FRANCD2, or BRACA-2, which in turn appears to interact with BRACA-1, which is believed to be activated by FANCD2.

  For the formation of FANCD2-L as a result of defects in the FA pathway at any time prior to post-translational modification of FANCD2, including FANCD2-S itself, in addition to defects based screening assays in the FANCD2 gene or protein Failure of the required ubiquitination reaction may be observed. Once the final step in the reaction is revealed, it is possible to prepare screening assays in which small molecules containing the “broken FA pathway” are screened intracellularly or in vitro until a molecule that repairs the broken pathway is found. Become. This molecule can then be used as a probe to identify the nature of the defect. This molecule can be further used as a therapeutic agent to repair defects. For example, the inventors have demonstrated that cell cycle arrest and reduced proliferation of FA cells can be corrected in part by overexpression of the protein SPHAR, a member of the cyclin family of proteins. This can form the basis of an assay that is suitable as a screen for identifying therapeutic small molecules.

  Cells that are deficient in post-translationally modified FANCD2 are particularly sensitive to DNA damage. These cells can serve as a sensitivity screen to determine whether a compound (including toxic molecules) has the ability to damage DNA. Conversely, these cells can also function as a sensitivity screen to determine whether a compound can protect cells from DNA damage.

  FA patients and patients suffering from syndromes associated with DNA repair defects die from complications of bone marrow failure. Gene transfer is a treatment option to correct this deficiency. Many defects may occur through the FA path. The inventors have demonstrated that the final step is crucial for the proper functioning of cells and organisms. In an embodiment of the invention, the correction of a defect in any of the FA pathways is a gene therapy or therapeutic that targets FANCD2-S transformation to FANCD2-L so that this transformation is successfully achieved. Can be achieved sufficiently.

  Gene therapy is described, for example, by Friedman in “Therapeutic for Genetic Disease”, T.M. It can be performed by generally accepted methods such as those described by Friedman, Oxford University Press (1991), p105-121. Tissues targeted for ex vivo or in vivo gene therapy include, for example, bone marrow, hematopoietic stem cells before the onset of anemia, and fetal tissue associated with developmental abnormalities. Gene therapy can provide wild type FAND2-L function to cells with a mutated FANCD2 allele. Providing such a function should suppress the tumor growth of the recipient cells or improve the symptoms of Fanconi anemia.

  The wild type FANCD-2 gene or part of the gene can be introduced into the cell with a vector such that the gene remains extrachromosomal. In such situations, the gene can be expressed by cells from an extrachromosomal location. When a portion of the gene is introduced into and expressed in a cell having a mutated FANCD-2 allele, the portion of the gene encodes a portion of the FANCD-2 protein that is required for non-tumor growth of the cell can do. Alternatively, the wild type FANCD-2 gene or part of the gene can be introduced into the mutant cell in such a way that it recombines with the endogenous mutant FANCD-2 gene present in the cell. it can.

  Viral vectors are a class of vectors for achieving gene therapy. Virus-mediated gene transfer can be combined with direct in vivo gene transfer using liposome delivery, allowing viral vectors to be directed to tumor cells rather than into surrounding non-dividing cells. Alternatively, viral vector producer cells can be injected into the tumor (Culver et al., 1992). The injection of producer cells will then provide a sustained source of vector particles. This technique has been approved for use in humans with inoperable brain tumors.

  The vector can be injected into the patient either locally to the tumor site or systemic (to reach any tumor cells that may have metastasized to other sites). If the transfected gene is not permanently incorporated into the genome of each target tumor cell, treatment must be repeated periodically.

  Gene transfer vectors for both recombination or extrachromosomal maintenance are known in the art (see, eg, US Pat. No. 5,252,479, International Patent Application No. 93/07282, and US Pat. Patent No. 6,303,379), viral vectors such as retrovirus, herpes virus (US Pat. No. 6,287,557) or adenovirus (US Pat. No. 6,281,010) or FANCD2-L Plasmid vectors are included.

  A vector having a therapeutic gene sequence or a DNA encoding said gene or part of said gene is injected into a patient either locally at the site of the tumor or systemically so that it can reach metastasized tumor cells Can do. Targeting can be accomplished without further manipulation of the vector, or the vector can be bound to a molecule that has binding specificity for the tumor, where such a molecule is a receptor agonist or antagonist. There can be and can further include peptides, lipids (including liposomes) or sugars including oligo- or polysaccharides, and synthetic targeting molecules. DNA can be bound to the binding ligand via polylysine. If the transfected gene is not permanently incorporated into the genome of each target tumor cell, treatment must be repeated periodically.

  Methods for introducing DNA into cells prior to introduction into a patient are described in the art (US Pat. No. 6,033,857), electroporation, calcium phosphate coprecipitation and viral transduction. It can be accomplished using techniques such as law, and the choice of the method is within the ability of one skilled in the art.

  Cells transformed with the wild-type or mutant FANCD2 gene are used as a model system to study disease remission resulting from defective DNA repair and drug therapy that promotes such remission it can.

  As generally discussed above, the FANCD2 gene, or fragment (if applicable) can be used in gene therapy to increase the amount of expression product of such gene in abnormal cells. Such gene therapy reduces the accumulation of defects that occur when FANCD2-L polypeptide levels are absent or reduced compared to normal cells, and where increased FANCD2-L levels result from defective DNA repair. It is particularly suitable for use in precancerous cells if it can be delayed and thus delay the onset of the cancerous condition. Such gene therapy is also useful for increasing the expression level of the FANCD2 gene, even in cells where the mutant gene is expressed at “normal” levels, but the level of the FANCD2-L isoform is reduced. There is something wrong. A crucial role of FANCD2-L in normal DNA repair is to provide an opportunity to develop therapeutic agents that correct defects that induce a decrease in the level of FANCD2-L. One approach to developing new therapeutics is through rational drug design. A rational drug design is a structural analog of a biologically active subject polypeptide or a small molecule (eg, agonist, antagonist, inhibitor or enhancer) that interacts with it. It can be provided to create an active or stable form or to design a small molecule that enhances or prevents the function of a polypeptide in vivo. Rational drug design can provide small molecules or modified polypeptides that have improved FANCD2-L activity or stability or function as enhancers, inhibitors, agonists, or antagonists of FANCD2-L activity. . The availability of cloned FANCD2 sequences can make available a sufficient amount of FANCD2-L polypeptide to perform analytical tests such as X-ray crystallography. Furthermore, the knowledge about the FANCD2-L protein sequence provided herein guides how to use computer-aided modeling methods instead of or in addition to X-ray crystallography.

  Peptides or other molecules having FANCD2-L activity can be supplied to cells that are deficient in protein in therapeutic preparations. The sequence of the FANCD2-L protein has been disclosed for several organisms (human, fly and plant) (SEQ ID NO: 1-3). FANCD2 can be produced, for example, by expressing a cDNA sequence in bacteria using known expression vectors with additional post-translational modifications. Alternatively, FANCD2-L polypeptide can be extracted from FANCD2-L producing mammalian cells. Furthermore, FANCD2-L protein can be synthesized using synthetic chemistry techniques. Other molecules with FANCD2-L activity (eg, peptides, drugs or organic compounds) can also be used as therapeutic agents. For peptide therapy, modified polypeptides having substantially similar functions are also used.

  Similarly, cells and animals that have mutant FANCD2 alleles or that produce insufficient levels of FANCD2-L can be used as model systems for studying and testing for potential therapeutic agents. . Cells that can be either somatic or germline can be isolated from individuals with reduced levels of FANCD2-L. Alternatively, as described above, cell lines with reduced levels of FANCD2-L can be engineered. After the test substance is applied to the cell, the transformed phenotype of the cell in which DNA repair is impaired is determined.

  The efficacy of the new candidate therapeutic molecule can be tested in laboratory animals for efficacy and lack of toxicity. Using standard techniques, animals can be selected to form transgenic animals after mutagenesis of all animals or after genetic manipulation of germline cells or zygotes. Such treatment usually includes the insertion of a mutated FANCD2 allele from a second animal species, as well as the insertion of a disrupted homologous gene. Alternatively, the animal's endogenous FANCD2 gene can be disrupted by insertion or deletion mutations or other genetic changes using conventional techniques (Capecchi, Science, (1989), vol. 244, p1288). ~ 1292) (Valancius and Smithies, 1991). After the test substance is administered to the animals, tumor growth must be assessed. If the test substance prevents or suppresses a pathology arising from defective DNA repair, the test substance is a candidate therapeutic for treating the disease identified here.

  The present invention provides a Fanconi anemia / BRCA based diagnostic assay to determine whether a patient has cancer or whether the patient is at increased risk of cancer. The invention also features screening methods for discovering novel cancer therapeutics that are inhibitors of the Fanconi anemia / BRCA pathway. Finally, the present invention provides methods of chemosensitizing tumor cells that are resistant to one or more chemotherapeutic compounds, as well as assays for determining the effectiveness of chemotherapeutic agents.

  The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology, cell biology, microbiology and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. For example, Sambrook, Fritsch & Maniatis, 1989, “Molecular Cloning: Experimental Manual, 2nd Edition (Molecular Cloning: A Laboratory Manual, Second Edition)”; “Synthesis of Oligonucleotides Science”. , 1984); "Nucleic Acid Hybridization" (BD Harnes & S. J. Higgins, 1984); "A Practical Guide to Molecular Cloning (A Practical Guide to Molecular Cloning)" (B. Perbal). , 1984); (Harlow, E. and La e, D.) “Use of Antibodies: Experimental Manuals: A Laboratory Manual (1999), Cold Spring Harbor Laboratory Press; and“ Methods in Enzymology (Ac.); “See Short Protocols in Molecular Biology (edited by Ausubel et al., 1995). All patents, patent applications, and publications mentioned herein, both above and below. Are incorporated by reference in their entirety.

The present invention relates to the preparation of cell extracts from patient biopsy tissue, including but not limited to brain, heart, lung, lymph node, eye, joint, skin and tumors associated with these organs. provide. “Tissue biopsy” also includes collections of biological fluids, including but not limited to blood, plasma, sputum, urine, cerebrospinal fluid, lavage fluid and leukophoresis samples. In a preferred embodiment, a “biopsy tissue” according to the present invention is taken from breast cancer, ovarian cancer, or prostate cancer. “Biopsy tissue” is obtained using techniques well known in the art, including needle aspiration and skin punch biopsy.

Cisplatin Cisplatin has been widely used to treat cancers such as metastatic testicular cancer or ovarian cancer, advanced bladder cancer, head and neck cancer, cervical cancer, lung cancer or other tumors. Cisplatin is an effective amount used in clinical applications, 15-20 mg / m ² and can be used alone or in combination with other drugs for a total of 3 courses, 5 days every 3 weeks. Typical ^{dose, 0.50mg / m 2, 1.0mg /} m 2, 1.50mg / m 2, 1.75mg / m 2, 2.0mg / m 2, 3.0mg / m 2, 4. It may be 0 mg / m ² , 5.0 mg / m ² , 10 mg / m ² . Of course, these doses are all examples and any dose between these points is expected to be used in the present invention. Cisplatin is not absorbed orally and must be delivered via intravenous, subcutaneous, intratumoral, or intraperitoneal injection. Proper handling and disposal procedures for anticancer drugs must be taken into account. Several guidelines on this issue have been published and are well known in the art.

  For example, PLATINOL-AQ, (cisplatin injection) NDC 0015-3220-22 (Bristol Myers Squibb) is supplied as a sterile multi-dose vial without preservatives. Each multi-dose vial contains 50 mg of cisplatin NDC 0015-3221-22 and must be stored protected from light at 15-25 ° C. The cisplatin remaining in the amber vial after the first use is stable for 28 days under shading and for 7 days under indoor fluorescent light.

Prescription information for PLATINOL-AQ, (cisplatin injection) NDC 0015-3220-22 is available from Bristol Myers Squibb. Plasma cisplatin concentration decreases monoexponentially after a bolus dose of 50 or 100 mg / m ² with a half-life of about 20-30 minutes. A single exponential decrease and a plasma half-life of about 0.5 hours are also seen after a 2 or 7 hour injection of 100 mg / m ² . Following the latter, systemic clearance and steady state distribution of cisplatin is about 15-16 L / h / m ² and 11-12 L / m ² .

Cisplatin dosage and application The dosage and application of cisplatin for cancer treatment is well known in the art. The prescription information for PLATINOL-AQ (Bristol Myers Squibb) recommends the following guidelines for dose and application: “Injections containing aluminum parts that may come into contact with PLATINOL-AQ for preparation or administration Do not use needles or intravenous sets. Aluminum reacts with PLATINOL-AQ causing precipitation and loss of effectiveness. "

Metastatic testicular cancer: The usual dose of PLATINOL-AQ for treating testicular cancer in combination with other approved chemotherapeutic agents is 20 mg / m ² (IV) daily for 5 days per cycle. It is.

Metastatic ovarian cancer: The usual dose of PLATINOL-AQ for treating metastatic ovarian cancer in combination with CYTOXAN (cyclophosphamide) is once every 4 weeks (Day 1), 75- 100 mg / m ² (IV). The dose of CYTOXAN when used in combination with PLATINOL-AQ is 600 mg / m ² (IV) once every four weeks (Day 1). Refer to the package insert of CYTOXAN for the administration method of CYTOXAN. In combination therapy, PLATINOL-AQ and CYTOXAN should be administered sequentially. In monotherapy, PLATINOL-AQ must be administered once every 4 weeks at a dose of 100 mg / m ² (IV) per cycle.

Advanced bladder cancer: PLATINOL-AQ (cisplatin injection) is once every 3-4 weeks, depending on the prior exposure to radiation therapy and / or the degree of prior chemotherapy, 50-70 mg per cycle / M ² (IV) should be administered as a single agent. For patients who have received large amounts of prior treatment, it is recommended to repeat an initial dose of 50 mg / m ² per cycle every 4 weeks. Hydration, a pretreatment by infusion of 1-2 liters of liquid 8-12 hours prior to PLATINOL-AQ administration, is recommended. The drug is then diluted in 2 liters of 5% dextrose in 1/2 or 1/3 saline containing 37.5 g mannitol and infused over 6-8 hours. If the diluted solution is not used within 6 hours, protect the solution from light. Do not dilute PLATINOL-AQ in just 5% dextrose injection. For the next 24 hours, proper water load and urine output must be maintained. Repeated PLATINOL-AQ courses should not be performed until serum creatinine is below 1.5 mg / 100 mL and / or BUN is below 25 mg / 100 mL. Repeated courses should not be performed until circulating blood elements are at acceptable levels (platelets> 100,000 / mm ² , WBC> 4,000 / mm ² ). Subsequent doses of PLATINOL-AQ should not be performed until the hearing analysis results indicate that hearing is within normal limits. As with other potentially toxic compounds, care must be taken when handling aqueous solutions. Skin reactions associated with accidental exposure to cisplatin may occur. The use of gloves is recommended. This aqueous solution should be used only by intravenous administration and should be administered by IV injection over 6-8 hours.

Chemosensitizer Dosages and Usage Methods of cancer sensitization are reported in US Pat. No. 5,776,925, which is incorporated herein in its entirety. The cancer treatment according to the present invention envisions the use of one or more anti-tumor agents in combination with a compound that modifies the host or tumor so that it is not necessarily cytotoxic per se, but can enhance anti-cancer therapy. Such agents are called chemosensitizers.

  Treatment with a chemosensitizer is according to the invention treatment in the presence of an antitumor agent and the corresponding chemosensitizer in the presence of an antitumor agent but no corresponding chemosensitizer. If the tumor size is reduced by 10%, preferably 25%, preferably 50%, more preferably 75%, most preferably 100% compared to the subsequent tumor size, it is therapeutically effective in cancer patients It is.

  The present invention provides a pharmaceutical composition comprising a therapeutically effective amount of a chemosensitizer in combination with a pharmaceutically acceptable carrier or excipient as disclosed herein. The chemosensitizer according to the present invention can be administered to a patient locally or in a systemic manner either intravenously, subcutaneously, intramuscularly, parenterally, intraperitoneally or orally. Preferably, administration is systemic with or prior to administration of one or more anti-tumor agents. In a preferred embodiment, the anti-tumor agent is cisplatin, which is well known in the art and is administered by a protocol as described herein.

  For oral administration, chemosensitizers useful in the present invention can generally be provided in the form of tablets or capsules, as powders or granules, or as an aqueous solution or suspension. Tablets for oral administration are mixed with pharmaceutically acceptable excipients such as inert diluents, disintegrants, binders, lubricants, sweeteners, flavoring agents, coloring agents and preservatives. Ingredients can be included. Suitable inert diluents include sodium carbonate, calcium carbonate, sodium phosphate, calcium phosphate, and lactose, and suitable disintegrants are corn starch and alginic acid. Binders include starch and gelatin, and the lubricant, if present, is generally magnesium stearate, stearic acid or talc. Tablets may be coated with a substance such as glyceryl monostearate or glyceryl distearate, if desired, to delay absorption in the gastrointestinal tract.

  Capsules for oral administration include hard gelatin capsules in which the active ingredient is mixed with a solid diluent, and soft gelatin capsules in which the active ingredient is mixed with water or fats such as peanut oil, liquid paraffin or olive oil. included.

  For subcutaneous and intravenous use, the chemosensitizers of the invention can be provided dissolved in a sterile aqueous solution or suspension treated with a buffer to an appropriate pH and isotonicity. Suitable aqueous excipients include Ringer's solution and isotonic sodium chloride. Aqueous suspensions according to the present invention may include suspending agents such as cellulose derivatives, sodium alginate, polyvinyl-pyrrolidone and tragacanth gum, and wetting agents such as lecithin. Suitable preservatives for aqueous suspensions include ethyl p-hydroxybenzoate and n-propyl p-hydroxybenzoate.

  Useful chemosensitizers according to the present invention can also be presented as liposomal formulations.

  In general, a suitable dose is in the range of 0.01-100 mg / kg of recipient's body weight per day, preferably in the range of 0.2-10 mg / kg body weight per day. The desired dose is preferably provided once a day, but may be administered as 2, 3, 4, 5, 6 or more divided doses at appropriate intervals throughout the day. These divided doses can be administered in unit dosage forms containing, for example, 10 to 1,500 mg, preferably 20 to 1,000 mg, and most preferably 50 to 700 mg of active ingredient per unit dosage form. The dose of chemosensitizer useful according to the invention will vary depending on the condition being treated or prevented and the nature of the chemosensitizer used. Effective doses and in vivo half-life estimates for individual compounds included in the present invention are useful for in vivo testing using animal models such as the mouse model described herein or for adapting the method to larger mammals. Can be estimated based on

  In addition to their individual administration, the compounds useful according to the present invention can be administered in combination with other known chemosensitizers and antitumor agents as described herein. In any case, the physician administering the drug can adjust the dose and timing of drug administration based on the results observed using standard measures of cancer activity known in the art.

Non-limiting examples of antineoplastic agents antineoplastic agents, such as anti-microtubule agents, topoisomerase inhibitors, antimetabolites, mitotic inhibitors, alkylating agents, intercalating agents, agents capable of interfering with a signal transduction pathway, apoptosis , Drugs, and antibodies to other tumor-associated antigens (including naked antibodies, immunotoxins and radioconjugates). Examples of specific classes of anticancer agents are provided in detail as follows: eg antitubulin / antimicrotubule agents such as paclitaxel, vincristine, vinblastine, vindesine, vinorelbine, taxotere; eg topotecan, camptothecin, doxorubicin, etoposide, mitoxine Topoisomerase I inhibitors such as santron, daunorubicin, idarubicin, teniposide, amsacrine, epirubicin, melvalon, pyroxanthrone hydrochloride; for example 5-fluorouracil (5-FU), methotrexate, 6-mercaptopurine, 6-thioguanine, fludarabine phosphate Cytarabine / Ara-C, trimetrexate, gemcitabine, acivicin, alanosine, pyrazofurin, N-phosphorylacetyl-L-aspartic acid (ie PALA), pe Tostatin, 5-azacytidine, 5-aza 2′-deoxycytidine, ara-A, cladribine, 5-fluorouridine, FUDR, thiazofurin, N- [5- [N- (3,4-dihydro-2-methyl-4 -Oxoquinazolin-6-ylmethyl) -N-methylamino] -2-thenoyl] -L-glutamic acid and the like; for example cisplatin, carboplatin, mitomycin C, BCNU (ie carmustine), melphalan, thiotepa, busulfan, Alkylating agents such as chlorambucil, pricamycin, dacarbazine, ifosfamide phosphate, cyclophosphamide, nitrogen mustard, uracil mustard, pipbloman, 4-ipomenol; Agents that act via a mechanism of action; biological response modifiers that enhance anti-tumor responses such as interferon; apoptotic agents such as actinomycin D; and antiestrogens such as tamoxifen, or 4′-cyano Antihormonal agents such as antiandrogens such as -3- (4-fluorophenylsulfonyl) -2-hydroxy-2-methyl-3 '-(trifluoromethyl) propionanilide.

  The antitumor agent, according to the present invention, has a tumor size of 10%, preferably 25%, preferably 50%, more preferably 75%, most preferably compared to the tumor size before the start of treatment with the antitumor agent. If it falls 100%, it is useful for treatment in cancer patients.

  In yet another embodiment, the anti-tumor agent is according to the present invention preferably if the cancer patient remains released from the cancer, i.e. after the start of cancer treatment, preferably for 6 months, preferably for 1 year, more preferably If there is no detectable tumor for 2 years, and most preferably 5 years or more, it is therapeutically effective.

Inhibitors of Fanconi Anemia / BRCA Pathway According to the Invention Potential inhibitors of Fanconi anemia / BRCA pathway include organisms that disrupt expression or function of the Fanconi anemia / BRCA pathway gene or protein, as defined herein. Includes but is not limited to molecules. Potential inhibitors of Fanconi anemia / BRCA pathway include Fanconi anemia / BRCA pathway gene antisense nucleic acid (antisense Fanconi anemia / BRCA pathway gene RNA, oligonucleotide, modified oligonucleotide, RNAi), Fanconi anemia / BRCA pathway Includes dominant negative mutants of genes, and inhibitors of Fanconi anemia / BRCA pathway gene transcription, mRNA processing, mRNA transport, protein translation, protein modification, protein transport, nuclear transport, and Fanconi anemia / BRCA protein complex formation However, it is not limited to them.

  In the most preferred embodiment, the present invention provides small molecule inhibitors of FANC-D2 ubiquitin E3 ligase.

To identify a microarray cancer therapeutic or chemosensitizer according to the present invention, the present invention provides the use of a microarray.

  In certain embodiments, the microarrays of the invention are used to identify chemosensitizers.

  In another embodiment, the microarray of the invention is used to test a biopsy tissue sample for the presence of a cancer-related defect within a Fanconi anemia / BRCA pathway gene.

  In another embodiment, the microarrays of the invention are used to screen for inhibitors of Fanconi anemia / BRCA gene pathway.

  In another embodiment, the microarrays of the invention are used to screen for inhibitors of FANC-D2 ubiquitin E3 ligase.

  In another embodiment, the invention may have cancer or be at risk of cancer screening for the presence of a cancer-related defect within the Fanconi anemia / BRCA gene pathway, as defined herein. A tissue microarray is provided that includes a biopsy tissue sample from a patient. In a preferred embodiment, the tissue microarray of the invention is used to screen for the presence of monoubiquitinated FANCD2-L.

  In yet another embodiment, the present invention provides a tissue microarray comprising biopsy tissue samples from patients having BRCA-1 and BRCA-2 / FANCD-1 cancer-related defects.

  In yet another embodiment, the present invention provides a tissue microarray comprising biopsy tissue samples from patients who do not have BRCA-1 and BRCA-2 / FANCD-1 cancer-related defects.

  A “sequencing array” contains a region of the entire open reading frame of the gene to search for mutations in a clinical sample. A “transcriptional profiling array” can have sequences from the 3 ′ end of the gene to measure mRNA expression in a clinical sample.

  A transcription profiling array can be used to examine the mRNA levels corresponding to each gene in the pathway. For example, breast cancer or ovarian cancer in which one of the transcripts corresponding to, for example, FANCF is reduced indicates that there is a defect in the Fanconi anemia / BRCA pathway due to reduced FANCF expression.

Construction of microarray
Microarray Substrate In certain embodiments of the invention, the microarray or array includes a substrate that facilitates handling of the microarray through various molecular techniques. As used herein, “molecular procedure” means contacting a microarray with a test reagent such as an antibody, nucleic acid probe, enzyme, chromogen, label, or molecular probe. In certain embodiments, the molecular approach includes multiple hybridizations, incubations, fixation steps, temperature changes (from 4 ° C. to 100 ° C.), solvent exposure, and / or washing steps.

  In yet another embodiment of the invention, the microarray is a substrate for facilitating exposure of a biopsy tissue sample to various potential inhibitors of the Fanconi anemia / BRCA pathway, cancer therapeutics or chemosensitizers. Is included.

In certain embodiments of the invention, the substrate of the microarray is solvent resistant. In another embodiment of the invention, the substrate is transparent. Substrates exist as particles, strands, sediments, gels, sheets, tubes, spheres, beads, containers, capillaries, pads, slices, films, plates, slides, chips, biological, non-biological, organic , Inorganic, or any combination thereof. The substrate is preferably flat or planar, but may take on a variety of other surface structures. Substrate is polymerized Langmuir-Blodgett (Langmuir Blodgett) film, functionalized _{glass, Si, Ge, GaAs, GaP} , Si0 2, SIN4, modified silicone or other non-porous substrates; polyolefins, polyamides, polyacrylamides, Plastics such as polyester, polyacrylic ester, polycarbonate, polytetrafluoroethylene, polyvinyl acetate; and plastic compositions containing fillers (such as glass fillers), extenders, stabilizers, and / or antioxidants; It may be a celluloid, cellophane or urea formaldehyde resin, or other synthetic resin such as cellulose acetate, ethyl cellulose, or other transparent polymer. Other substrate materials will be readily apparent to those of skill in the art upon reviewing the present disclosure.

  In some embodiments, the microarray substrate is rigid; however, in other embodiments, the profile array substrate is semi-rigid or flexible (eg, polycarbonate, cellulose acetate, polyvinyl chloride, etc.). In yet another embodiment, the array substrate is optically opaque and substantially non-fluorescent. Nylon or nitrocellulose membranes can also be used as array substrates, including polycarbonate, polyvinylidene fluoride (PVDF), polysulfone, mixed esters of cellulose and nitrocellulose, and the like.

  The size and shape of the substrate can generally vary. The substrate may have a convenient shape such as a disc shape, a quadrangle, a sphere, or a circle. Preferably, however, the substrate fits perfectly on the microscope stage. In one embodiment, the profile array substrate is planar. In certain embodiments of the invention, the microarray substrate is 1 inch × 3 inches, 77 × 50 mm, or 22 × 50 mm. In another embodiment of the invention, the microarray substrate is at least 10-200 mm x 10-200 mm.

Additional features of the substrate In certain embodiments of the invention, the substrate is a microchip for transmitting an identification factor (e.g., colored pencil or crayon mark, etched mark, sign, bar code, radio signal or electrical signal). Etc.) including a place to place. In one embodiment, the location includes ground glass. In certain embodiments, the microchip is associated with identity and sub-location addresses on the array and / or collected by tissues such as prognosis, diagnosis, medical history, family medical history, drug therapy, age of death and cause of death Communicating with a processor that contains or has access to stored information, including information about the person who has been placed.

The sub-position microarray includes a plurality of sub-positions. Each sub-position contains tissue associated with them (eg, that position can be retained relative to another sub-position after exposure to at least one molecular approach). In certain embodiments, the tissue is visible at least under a microscope to distinguish subcellular features (eg, nuclei, intact cell membranes, organelles, and / or other cytological features), ie, the tissue is lysed. Tissue with substantially intact morphological characteristics.

  In some embodiments of the invention, the microarray includes 2-1,000 sub-positions. In yet another embodiment, the microarray is 2, 5, 10, 20, 25, 30, 45, 50, 55, 60, 65, 75, 100, 150, 200, 250, 500, 550, 600, 650, 700. , 750, 800, 850, 900, 950 or more than 1,000 sub-positions. In some embodiments of the invention, each sub-position is 2-10 mm apart. In yet another embodiment of the invention, each sub-position includes at least one dimension that is 20-600 mm. The sub-positions can be configured in any pattern, and each sub-position can generally be any shape (square, circular, elliptical, oval, disk-shaped, rectangular, triangular, etc.).

  In a preferred embodiment, the sub-positions are arranged in a regular repeating pattern (eg, rows and columns) to ensure the identification of each sub-position with respect to tissue type can be ensured by use of an array detector. In one embodiment, the array detector is a template that has a plurality of shapes, each shape corresponding to the shape of each sub-position in the array, and maintains the same relationship with each sub-position on the array. is there. The array detector is marked with coordinates that allow the user to easily identify sub-positions on the array with unique coordinates. In some embodiments of the invention, the array detector is a transparent sheet (eg, plastic, acetate, etc.). In another embodiment of the present invention, the array detector is a sheet that includes a plurality of holes, each hole corresponding to a shape and position to each sub-position on the array.

  In one aspect, the invention provides an array, wherein the compound comprising the array is spotted on a solid support, such as spotted using a robotic GMS417 arrayer (Affymetrix, CA). Is done. Alternatively, spotting can be performed using contact printing techniques or other methods known in the art.

Microarray types according to the invention
Small molecule array In the small molecule microarray or array of the present invention, the small molecule is stably associated with the surface of the solid support, wherein the support may be a flexible or rigid solid support. “Stablely associated” means that each small molecule maintains a unique position relative to a solid support under binding and wash conditions. Thus, the sample is stably and non-covalently or covalently associated with the support surface. Examples of non-covalent binding include non-specific adsorption, binding based on electrostatic interactions (eg, ion-pair interactions), hydrophobic interactions, hydrogen bonding interactions, covalently attached to the support surface Specific binding via a specific binding pair member and the like are included. Examples of covalent bonds include covalent bonds formed between a small molecule and a functional group (eg, --OH) present on the surface of the rigid support, where the functional group is in its native form. It may be. It will be understood that although the surface of the substrate can preferably be provided with a layer of linker molecules, the linker molecules are not a required element of the present invention. The linker molecule is preferably of sufficient length for the small molecules of the invention and on the substrate to bind freely to and interact with molecules exposed to the substrate.

The amount of small molecule present in each composition will be sufficient to provide proper binding and detection of the target small molecule during the assay in which the array is used. Generally, the amount of each small molecule that is stably associated with the solid support of the array is at least about 0.1 pg, preferably at least about 0.5 pg, and more preferably at least about 1 pg, but this amount May be as high as 1,000 pg or more, but usually does not exceed about 100 pg. In preferred embodiments, the microarray has a density greater than 1, 2, 5, 7, 10, 15 or 20 small molecules / cm ² or more.

Tissue Microarray In a preferred embodiment of the invention, the microarray or array comprises a human tissue sample. A microarray according to the present invention includes a plurality of sub-locations, each containing a tissue sample having at least one known biological characteristic (eg, tissue type, etc.). In a preferred embodiment of the invention, the plurality of sub-locations comprises cancerous tissue in various tumor stages.

  In certain embodiments of the invention, the cancerous cells in the individual sub-locations are from an underlying cancer or an individual who is predisposed to have cancer.

  In certain embodiments of the invention, the cancerous cells in individual sub-locations are from individuals with a cancer-related defect in the BRCA-1 and / or FANCD1 / BRCA-2 genes.

  In certain embodiments, the microarray includes at least one sub-location that includes cancerous cells from a single patient and includes a plurality of sub-locations that include cells from other tissues and organs from the same patient. In another embodiment, from multiple individuals who all died due to the same pathology, or from individuals being treated with the same drug, including individuals who have recovered from and / or have not recovered from the disease A microarray comprising a plurality of cells is provided.

  In another embodiment of the present invention, the microarray includes a plurality of sub-locations that include cells from individuals who share traits in addition to cancer. In certain embodiments of the invention, the shared trait is gender, age, pathology, predisposition to pathology, exposure to infectious disease (eg, HIV), relatedness, death from the same disease, treatment with the same drug, Exposure to chemotherapy or radiation therapy, exposure to hormonal therapy, exposure to surgery, exposure to the same environmental conditions, identical genetic changes or groups of changes, expression of the same genes or groups of genes.

  In yet another embodiment of the present invention, each sub-location of the microarray includes various members of the family that share a family history of cancer (eg, siblings, twins, cousins (cousins), mother, father, grandmother, grandfather, uncle ( Cell) derived from a group consisting of (uncle), aunt (aunt) and the like. In yet another embodiment of the invention, a “pedigree microarray” includes environmentally matched controls (eg, husband, wife, adopted child, stepfather / stepmother, etc.). In yet another embodiment of the invention, the microarray is, for example, an overweight smoker, a diabetic patient with peripheral vascular disease, a disease (eg, sickle cell anemia, Tay-Sachs disease, severe combined immunodeficiency). This is a reflection of a plurality of traits that represent a demographic population of a particular patient of interest, such as an individual with a specific predisposition to, but at this time the individuals included in each group have cancer.

  In a preferred embodiment of the present invention, the microarray includes human biopsy tissue.

  FANCD2 − / − as disclosed herein. In one embodiment, the microarray includes a plurality of tissues from such mice. In another embodiment of the invention, the microarray is FANCD2 − / − as disclosed herein and is treated with a cancer treatment (eg, drug, antibody, protein therapy, gene therapy, antisense therapy, etc.). Including mouse-derived tissue.

Screening for chemosensitizers and novel cancer therapeutics The microarrays of the present invention are used to screen for chemosensitizers and cancer therapeutics. The screening method used is disclosed in Examples 15 and 16.

Measurement of resistance to chemosensitizer Methylation of the FANCF gene in tumor cells treated with cisplatin results in suppression of FANCF gene expression and thereby disrupts the DNA damage repair mechanism of the tumor cells, Give rise to tolerance. Thus, the present invention provides a method for determining the methylation status of any of the Fanconi anemia / BRCA pathway genes (see Example 19). In a preferred embodiment, the present invention uses one or more chemotherapeutic compounds to determine the methylation status of Fanconi anemia / BRCA gene as a measure of the degree of tumor resistance to one or more chemotherapeutic compounds. A microarray of biopsy tissue samples from a patient being treated is provided. Methods for measuring DNA methylation of genes are well known in the art (see US Pat. Nos. 6,200,756; 6,331,393; 6,251,594).

Kits According to the Invention The present invention is a kit useful for screening for chemosensitizers and cancer therapeutics, and for diagnosing a cancer or predisposition to cancer associated with a cancer-related defect in the Fanconi anemia / BRCA gene pathway. Useful kits are provided. Useful kits according to the invention include isolated FANCD2 polynucleotide primer pairs, probes and inhibitors of the Fanconi anemia / BRCA pathway, and FANCD2-specific antibodies. In addition, the kit can contain a control unmethylated FANCD2 gene. In yet another embodiment, a kit according to the invention may contain an ovarian cancer tumor cell line. All kits according to the present invention comprise the above items or combinations of items and packaging materials therefor. The kit also includes instructions for use.

  The present invention will be described with reference to the following examples, which are provided by way of illustration and are not intended to limit the invention in any way. Standard techniques known in the art or the techniques described in detail below were utilized.

Example
Example 1: Experimental protocol used in Examples 2-8 Cell line and culture conditions. Epstein-Barr virus (EBV) transformed lymphoblasts are maintained in RPMI medium supplemented with 15% heat-inactivated fetal calf serum (FCS) and grown in a humidified atmosphere at 37 ° C. containing 5% CO _2. It was. Control lymphoblastic line (PD7) and FA lymphoblastic lineage (FA-A (HSC72), FA-C (PD-4), FA-D (PD-20), FA-F (EUFA121)), and FA- G (EUFA316)) has been previously described (de Winter et al., Nat. Genet., (1998), vol. 20, p281-283) (Whitney et al., Nat. Genet., (1995) vol.11. 341-343) (Yamashita et al., PNS AS, (1994) vol. 91, 6712-6716) (de Winter et al., Am. J. Hum. Genet., (2001), vol. 57). 1306-1308). PD81 is a lymphoblast cell line derived from a FA-A patient. SV40 transformed FA fibroblasts GM6914, PD426, FAG326SV and PD20F and HeLa cells were grown in DMEM supplemented with 15% FCS. FA cells (both lymphoblasts and fibroblasts) were functionally complemented with the pMMP retroviral vector containing the corresponding FANC cDNA, and functional complementation was confirmed by the MMC assay (Garcia-Higuera Et al., Mol.Cell.Biol., (1999) vol.19, p4866-4873) (Kuang et al., Blood, (2000), vol.96, p1625-1632).

  Cell cycle synchronization. HeLa cells, GM6914 cells, and GM6914 cells corrected with pMMP-FANCA retrovirus were synchronized by the previously described double thymidine block method with minor modifications (Kupfer et al., Blood, (1997). , Vol. 90, p1047-1054). Briefly, cells are 18 hours with 2 mM thymidine, 10 hours with thymidine-free medium, and 18 hours with additional 2 mM thymidine to arrest the cell cycle at the G1 / S boundary phase. Processed. Cells were washed twice with PBS, then released in DMEM + 15% FCS and analyzed at various time intervals.

  Alternatively, HeLa cells are treated with 0.5 mM mimosine (Sigma) for 24 hours to synchronize in late G1 phase (Krude, 1999), washed twice with PBS and released in DMEM + 15% FCS I let you. The nocodazole block method was used for synchronization in the M phase (Ruffner et al., Mol. Cell. Biol., (1999), vol. 19, p4843-4854). Cells were treated with 0.1 μg / mL nocodazole (Sigma) for 15 hours, and non-adherent cells were washed twice with PBS and re-plated in DMEM + 15% FCS.

  Cell cycle analysis. Trypsinized cells were resuspended in 0.5 mL PBS and fixed by adding 5 mL ice-cold ethanol. The cells were then washed twice with PBS containing 1% bovine serum albumin fraction V (1% BSA / PBS) (Sigma) and resuspended in 0.24 mL of 1% BSA / PBS. After adding 30 μL of 500 μ / mL propidium iodide (Sigma) dissolved in 38 mM sodium citrate (pH 7.0) and 30 μL of 10 mg / mL DNase-free RNase A (Sigma), the sample was incubated at 37 ° C. for 30 minutes did. DNA content was measured by FACScan (Beckton Dickinson) and data was analyzed by CellQuest and Modfit LT program (Becton Dickinson).

  Generation of anti-FANCD2 antiserum. Rabbit polyclonal antisera against FANCD2 was generated using GST-FANCD2 (N-terminal) fusion protein as the antigen source. The 5 ′ fragment was obtained from the full-length PCR polymerase using the primers (SEQ ID NO: 95) DF4EcoRI (5′AGCCTCgaattcGTTCTCAAAAGAAGACTGTCA-3 ′) and (SEQ ID NO: 96) DR816Xh (5′-GGTATCctcgagTCAAGACGACACTTATCCATCA-3 ′) ). The resulting 841 bp PCR product encoding the amino terminal 272 amino acids of the FANCD2 polypeptide was digested with EcoRI / XhoI and subcloned into the EcoRI / XhoI site of plasmid pGEX4T-1 (Pharmacia). A GST-FANCD2 (N-terminal) fusion protein of expected size (54 kD) is expressed in E. coli strain DH5γ, purified with glutathione-S-Sepharose and used to immunize New Zealand white rabbits did. FANCD2-specific immune antisera were affinity purified by passing through an AminoLink Plus column (Pierce) loaded with GST protein and through an AminoLink Plus column loaded with GST-FANCD2 (N-terminal) fusion protein.

  Generation of anti-FANCD2 MoAbs. Two anti-FANCD2 monoclonal antibodies were generated as follows. Balb / c mice were immunized with a GST-FANCD2 (N-terminal) fusion protein, which was the same fusion protein used to generate rabbit polyclonal antiserum (E35) to FANCD2. Animals were boosted with immunogen for 4 days prior to fusion, splenocytes were harvested, and hybridization with myeloma cells was performed. Hybridoma supernatants were collected and assayed using a standard ELISA assay as an initial screen and FANCD2 immunoblot analysis as a secondary screen. Two anti-human FANCD2 monoclonal antibodies (MoAbs) (FI17 and FI14) were selected for subsequent studies. Hybridoma supernatants from two positive cell lines were clarified by centrifugation. The supernatant was used as MoAbs for Western blotting. MoAbs were purified using an affinity column for IgG. MoAbs were stored as a 0.5 mg / mL stock in phosphate buffered saline (PBS). Anti-HA antibody (HA.11) was from Babco.

  Immunoblotting. Cells were lysed using 1 × sample buffer (50 mM Tris-HCl (pH 6.8), 86 mM 2-mercaptoethanol, 2% sodium dodecyl sulfate (SDS)), boiled for 5 minutes, and 7.5% Polyacrylamide SDS gel electrophoresis was performed. After electrophoresis, proteins were transferred to nitrocellulose using a submerged transfer device (BioRad) filled with 25 mM Tris base, 200 mM glycine, 20% methanol. After blocking with 5% non-fat dry milk in TBS-T (50 mM Tris-HCl (pH 8.0), 150 mM NaCl, 0.1% Tween 20), TBS-T (affinity purified anti-FANCD2 polyclonal antibody) Incubate the membrane with primary antibody diluted in (E35) or 1: 1000 dilution for anti-HA (HA.11), 1: 200 dilution for anti-FANCD2 mouse monoclonal antibody FI17). Washed thoroughly and incubated with appropriate horseradish peroxidase conjugated secondary antibody (Amersham). Chemiluminescence was used for detection.

  Generation of DNA damage. Gamma irradiation was performed using a Gamma cell 40 apparatus. UV exposure was achieved using Stratalinker (Stratagene) after gently aspirating the culture medium. For mitomycin C treatment, cells were exposed to this drug continuously for the indicated times. Hydroxyurea (Sigma) was added over 24 hours until the final concentration was 1 mM.

  Detection of monoubiquitinated FANCD2. HeLa cells (or FA-G fibroblasts, FAG326SV) were transfected with FuGENE6 (Roche) according to the manufacturer's protocol. HeLa cells were plated on 15 cm tissue culture dishes, and 15 μg of HA-tag labeled ubiquitin expression vector (pMT 123) (Treaier et al., Cell, (1994), vol. 78, p787-798) per culture dish. Used to transfect. Twelve hours after transfection, cells were treated with indicated concentrations of MMC (0, 10, 40, 160 ng / mL) or indicated doses of IR (0, 5, 10, 10, 20 Gy). After 24 hours incubation with MMC, or 2 hours after IR treatment, whole cell extracts were obtained from protease inhibitors (1 μg / mL leupeptin and pepstatin, 2 μg / mL aprotinin, 1 mM phenylmethylsulfonyl fluoride) and In lysis buffer (50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1% (v / v) Triton X-100) supplemented with a phosphatase inhibitor (1 mM sodium orthovanadate, 10 mM sodium fluoride) Prepared. Using a polyclonal antibody against FANCD2 (E35), immunoprecipitation (IP) was essentially described previously (Kupfer et al., 1997), except that each IP was standardized to contain 4 mg of protein. ). Pre-immune serum from the same rabbit was used as a negative control in the IP reaction. Immunoblotting was performed using anti-HA (HA.11) or anti-FANCD2 (FI17) monoclonal antibodies.

  Ubiquitin aldehyde treatment. HeLa cells were treated with 1 mM hydroxyurea for 24 hours and whole cell extracts were prepared in lysis buffer supplemented with protease inhibitors and phosphatase inhibitors. 200 μg of cell lysate in 67 μL reaction containing 6.7 μL of 25 μM ubiquitinaldehyde (Boston Biochem) or 6.7 μL DMSO in DMSO was incubated at 30 ° C. or 37 ° C. for the indicated period. To each sample was added 67 μL of 2 × sample buffer, the samples were boiled for 5 minutes, separated by 7.5% SDS-PAGE, and immunoblotted against FANCD2 using FI17 monoclonal anti-human FANCD2 antibody. .

  Immunofluorescence microscopy. Cells were fixed with 2% paraformaldehyde in PBS for 20 minutes followed by permeabilization with 0.3% Triton-X-100 in PBS (10 minutes). After blocking in 10% goat serum, 0.1% NP-40 (blocking buffer) dissolved in PBS, the specific antibody was added at an appropriate dilution in blocking buffer and allowed to stand at room temperature for 2-4 hours Incubated. FANCD2 was detected using affinity purified E35 polyclonal antibody (1/100). In order to detect BRCA1, a commercially available monoclonal antibody (D-9, Santa Cruz) was used at 2 μg / mL. Cells are subsequently washed 3 times in PBS + 0.1% NP-40 (10-15 min for each wash), and species-specific fluorescein or Texas Red conjugate secondary antibody (Jackson Immunoresearch) is diluted in blocking buffer ( Anti-mouse 1/200, anti-rabbit 1/1000). After 1 hour at room temperature, another 10-15 minute wash was performed three times and the slide was placed on a Vectashield (Vector laboratories). Images were recorded with a Nikon microscope and processed using Adobe Photoshop software.

  Staining of meiotic chromosomes. Surface smears of thick and double thread spermatocytes from 16-28 day old male mice were prepared as described (Peters et al., 1997). Polyclonal goat antibodies against mouse SCP3 protein were used to visualize axial and synaptonemal structures in meiotic preparations. M118 mouse monoclonal antibody against mouse BRCA1 was generated by standard techniques by immunizing mice with mouse BRCA1 protein. To detect FANCD, affinity purified E35 rabbit polyclonal antibody was used at a dilution of 1: 200. Antibody incubation and detection methods are as described by (Keegan et al., Genes Dev., (1996), vol. 10, p2423- 2437) (Moens et al., J. Cell. Biol., (1987), vol. 105, p93-103). For detection, a combination of donkey-anti-mouse IgG-FITC-conjugated, donkey-anti-rabbit IgG-TRITC-conjugated, and donkey-anti-goat IgG Cy5-conjugated secondary antibody was used (Jackson ImmunoResearch Laboratories). All preparations were counterstained with 4 ', 6' diamino-2-phenylindole (DAPI, Sigma) and placed in DABCO (Sigma) antifade solution. The preparations were examined with a Nikon E1000 microscope (60X CFI plan apochromat and 100X CR planfluor oil immersion objective). Each fluorochrome (FITC, TRITC, Cy5 and DAPI) image was recorded individually as a 800 × 1000 pixel 12-bit source image via IPLab software (Scannalytics) controlling a cooled CCD camera (Princeton Instruments MicroMax), Individual 12-bit grayscale images were resampled, 24-bit pseudo color images, and combined using Adobe Photoshop.

Example 2: FA gene interacts in a common cellular pathway Normal lymphoblasts are two isoforms of FANCD2 protein, short chain (FANCD2-S, 155 kD) and long chain (FANCD2-L, 162 kD) Is expressed. FIG. 1 shows what happens when a whole cell extract is prepared from a lymphoblast system and cellular proteins are immunoprecipitated using anti-FANCD2 antiserum. Normal wild type cells express two isoforms of the FANCD2 protein, the low molecular weight isoform FANCD2-S (155 kD isoform) and the high molecular weight isoform FANCD2-L (162 kD isoform). FANCD2-S is the primary translation product of cloned FANCD2 cDNA. We next evaluated a series of large FA lymphoblasts and fibroblasts for expression of the FANCD2 isoform (Table 5). Correction of these FA cell lines with the corresponding FA cDNA resulted in functional complementation and repair of the high molecular weight isoform FANCD2-L.

  As previously described, FA cells are sensitive to the DNA cross-linking agent MMC, and in some cases to ionizing radiation (IR). Interestingly, FA cells from multiple complementation groups (A, C, G, and F) expressed only the FANCD2-S isoform (FIG. 1A, lanes 3, 7, 9, 11). FA cells from the B and E complementation groups also express only FANCD2-S. Functional correction of MMC and IR sensitivity of these FA cells with the corresponding FANC cDNA restores the FA protein complex (Garcia-Higuera et al., 1999) and restores the high molecular weight isoform (FANCD2-L) (FIG. 1A, lanes 4, 8, 10, 12). Taken together, these results demonstrate that the FA protein complex containing FANCA, FANCC, FANCF, and FANCG directly or indirectly regulates the expression of the two isoforms of FANCD2. For this reason, six cloned FA genes appear to interact in a common pathway.

Example 3: FA protein complex is required for monoubiquitination of FANCD2 High molecular weight isoforms of FANCD2 include alternative splicing of FANCD2 mRNA or post-translational modification of FANCD2 protein from one or more mechanisms Could be generated. Treatment with phosphatase does not convert FANCD2-L to FANCD2-S, demonstrating that phosphorylation alone does not contribute to the observed differences in their molecular weight.

  To identify other possible post-translational modifications of FANCD2, we first explored cellular conditions that regulate the conversion of FANCD2-S to FANCD2-L (FIGS. 1B, C). Since FA cells are sensitive to MMC and IR, it was inferred that these substances may regulate the conversion of FANCD2-S to FANCD2-L in normal cells. Interestingly, HeLa cells treated with MMC (FIG. 1B, lanes 1-6) or IR (FIG. 1C, lanes 1-6) showed a dose-dependent increase in the expression of FANCD2-L isoforms.

  In order to determine whether FANCD2-L is a ubiquitinated isoform of FANCD2-S, we transfected HeLa cells with cDNA encoding HA-ubiquitin (Treier et al., 1994). . Exposure of cells to MMC (FIG. 1B, lanes 7-10) or IR (FIG. 1C, lanes 7-10) caused a dose-dependent increase in FANCD2 HA-ubiquitin binding. Only the FANCD2-L isoform was immunoreactive with the anti-HA antibody and the FANCD2-S isoform was not immunoreactive. FANCD2 was not ubiquitinated in FA cells, but FANCD2 ubiquitination was restored when these cells were functionally complemented. FANCD2 was not ubiquitinated in FA cells, but FANCD2 ubiquitination was restored when these cells were functionally complemented. Since the FANCD2-S and FANCD2-L isoforms differ by 7 kD, FANCD2-L probably contains a single ubiquitin moiety (76 amino acids) covalently linked by an amide bond to the internal lysine residue of FANCD2. doing.

  To confirm monoubiquitination, we isolated FANCD2-L protein from HeLa cells and analyzed its trypsin fragment by mass spectrometry (Wu et al., Science, (2000), vol. 289, p11a). ). The ubiquitin / trypsin fragment could be clearly identified, and the monoubiquitination site (K561 of FANCD2) could also be identified. Interestingly, this lysine residue is human, Drosophila, and C.I. Conserved among the FANCD2 sequences from elegance (a type of nematode), this suggests that ubiquitination at this site is important for the FA pathway in multiple organisms. Mutation of this lysine residue, FANCD2 (K561R), resulted in loss of FANCD2 monoubiquitination.

Example 4: Intranuclear focus formation containing FANCD2 requires an intact FA pathway We have found that FANCD2 protein in uncorrected MMC-sensitive FA fibroblasts and functionally complemented fibroblasts Were tested for immunofluorescence patterns (FIG. 2).

  Corrected FA cells expressed both FANCD2-S and FANCD2-L isoforms (FIG. 2A, lanes 2, 4, 6, 8). Endogenous FANCD2 protein was observed exclusively in the nuclei of human cells and cytoplasmic staining was not evident (FIG. 2B, ah). PD-20 (FA-D) cells reduced nuclear immunofluorescence (FIG. 2B, d), consistent with reduced expression of FANCD2 protein in these cells by immunoblotting (FIG. 2A, lane 7). . In PD20 cells functionally corrected using the FANCD2 gene by the chromosomal transfer method, the FANCD2 protein was stained with two nuclear patterns. The majority of corrected cells had a diffusible nuclear pattern of staining, and a small fraction of cells stained for intranuclear focus (see dots, panel h). Both nuclear patterns were observed using three independently obtained anti-FANCD2 antisera (one polyclonal and two monoclonal antisera). FA fibroblasts from subtypes A, G, and C showed only a diffusive pattern of FANCD2 nuclear immunofluorescence. Functional complementation of these cells with FANCA, FANCG, or FANCC cDNA restored the MMC resistance of these cells, respectively (Table 6) and restored nuclear focus in some cells. Thus, the presence of high molecular weight FANCD2-L isoforms correlates with the presence of FANCD2 intranuclear foci, suggesting that only monoubiquitinated FANCD2-L isoforms are selectively localized to these foci. doing.

Example 5: The FANCD2 protein localizes to the nuclear focus during the S phase of the cell cycle. Since only one fraction of asynchronously functionally complemented cells contained FANCD2 nuclear focus, this The inventors speculated that these foci may gather at discrete points in the cell cycle. To test this hypothesis, we tested for the generation of FANCD2-L isoforms and FANCD2 nuclear foci in synchronized cells (FIG. 3). HeLa cells were synchronized at the G1 / S boundary phase, released to S phase, and analyzed for the generation of FANCD2-L isoform (FIG. 3A). The FANCD2-L isoform was specifically expressed during late G1 and throughout S phase. Synchronized, uncomplemented FA cells (FA-A fibroblasts, GM6914) expressed normal to increased levels of FANCD2-S protein, but did not express FANCD2-L at any time during the cell cycle. It could not be expressed. Functional complementation of these FA-A cells by stable transfection with FANCA cDNA restored S phase specific expression of FANCD2-L. S phase specific expression of the FANCD2-L isoform was confirmed when HeLa cells were synchronized by other methods such as nocodazole arrest (FIG. 3B) or mimosine exposure (FIG. 3B). Cells arrested at mitosis did not express FANCD2-L, suggesting that the FANCD2-L isoform has been removed or degraded prior to cell division (FIG. 3B). Mitosis). Taken together, these results demonstrate that the monoubiquitination of the FANCD2 protein is highly regulated during the cell cycle and that this modification requires the intact FA pathway.

  Cell cycle-dependent expression of the FANCD2-L isoform was also correlated with the generation of FANCD2 nuclear foci (FIG. 3C). Nocodazole-arrested (mitotic) cells do not express the FANCD2-L isoform and do not show FANCD2 nuclear focus (FIG. 3C, 0 hours). When these synchronized cells were moved beyond S phase (15-18 hours), an increase in FANCD2 nuclear focus was observed.

Example 6: FANCD2 protein localizes to nuclear foci in response to DNA damage We tested for the accumulation of FANCD2-L isoforms and FANCD2 nuclear foci in response to DNA damage (FIG. 4). ). Previous studies have shown that FA cells are sensitive to substances that cause DNA interstrand cross-linking (MMC) or double-strand breaks (IR), but are relatively insensitive to ultraviolet (UV) and monofunctional alkylating agents. Proven to be resistant. MMC activated FANCD2-S to FANCD2-L conversion in unsynchronized HeLa cells (FIG. 4A). The highest conversion to FANCD2-L occurred 12-24 hours after MMC exposure, which correlated with the time of highest FANCD2 nuclear focus generation. An increase in FANCD2 nuclear focus corresponding to an increase in FANCD2-L occurred. Ionizing radiation also activated a time-dependent and dose-dependent increase in FANCD2-L in HeLa cells, with a corresponding increase in FANCD2 focus (FIG. 4B). Surprisingly, ultraviolet (UV) light activated a time-dependent and dose-dependent increase from FANCD2-S to FANCD2-L with a corresponding increase in FANCD2 focus (FIG. 4C).

  We tested the effect of DNA damage on FA cells (FIG. 4D). FA cells from multiple complementation groups (A, C, and G) failed to activate the FANCD2-L isoform in response to MMC or IR exposure, and failed to activate the FANCD2 nuclear focus. These data suggest that the cellular sensitivity of FA cells arises, at least in part, from their failure to activate FANCD2-L and FANCD2 nuclear foci.

Example 7: Co-localization of activated FANCD2 and BRCA1 proteins Like FANCD2, the breast cancer sensitive protein BRCA1 is upregulated in proliferating cells and responds to post-translational modifications during S phase or to DNA damage Activated. BRCA has a carboxy-terminal 20 amino acid containing a highly acidic HMG-like domain, suggesting a possible mechanism for chromatin repair. The BRCA1 protein co-localizes with IR-induced focus (IRIF) along with other proteins involved in DNA repair such as RAD51 or NBS / Mre11 / RAD50 complex. Cells with biallelic mutations in BRCA1 have defects in DNA repair and are sensitive to DNA damaging agents such as IR and MMC (Table 5). Taken together, these data suggest a possible functional interaction between FANCD2 and BRCA1 proteins. The BRCA focus is a large (2 mDa) multiple protein complex containing ATM and ATM substrates involved in DNA repair (BRCA1) and checkpoint function (NBS).

  To determine whether the activated FANCD2 protein co-localizes with the BRCA1 protein, we performed a double immunolabeling method for HeLa cells (FIG. 5). In the absence of ionizing radiation, approximately 30-50% of cells contained BRCA1 nuclear foci (FIG. 5A). In contrast, only rare cells beyond S phase contained FANCD2 dots (b, e). These nuclear foci were also immunoreactive with antisera to both BRCA1 and FANCD2 (c, f). After IR exposure, an increase in the number of cells containing nuclear foci and the number of foci per cell occurred. These intranuclear foci were larger and more fluorescent than those observed in the absence of IR. In addition, these nuclear foci contained both BRCA1 and FANCD2 proteins (i, l). The interaction between FANCD2-L and BRCA1 was further confirmed by protein co-immunoprecipitation reaction from exponentially growing HeLa cells exposed to IR (FIG. 5B).

  We tested the effect of BRCA1 expression on the generation of FANCD2-L and nuclear focus (FIG. 6). The BRCA1 (− / −) cell line, HCC1937, expresses a mutated form of the BRCA1 protein containing a carboxy terminal truncation. Although these cells expressed low levels of FANCD2-L (FIG. 6A), IR was unable to activate the increase in FANCD2-L levels. Furthermore, these cells reduced the number of IR-induced FANCD2 foci (FIG. 6B, panels c, d). Correction of these BRCA1 (− / −) cells by stable transfection with BRCA1 cDNA restored IR-induced FANCD2 ubiquitination and nuclear focus (FIG. 6B, panels k, l). These data suggest that wild-type BRCA1 protein is required as an “organizer” for IR-induced FANCD2 dot generation, and further suggest a functional interaction between these proteins Yes.

Example 8: Co-localization of FANCD2 and BRCA1 on meiotic chromosomes The association of FANCD2 and BRCA1 in meiotic cells may also cause these proteins to co-localize during premeiosis. I suggested that. Previous studies have demonstrated that BRCA1 protein is concentrated on the non-synaptic / axial structure of human synaptonemal structures in the mating and thick spermatocytes. In order to test for possible co-localization of FANCD2 and BRCA1 in meiotic cells, we were able to determine the presence of FANCD2 and BRCA1 protein in late mitotic and early bifilament mouse spermatocytes. The surface smear was tested (FIG. 7). We have shown that the rabbit polyclonal anti-FANCD2 antibody E35 specifically stains the unpaired axes of the X and Y chromosomes at the late typhoon stage (FIG. 7a) and the double thread stage (FIGS. 7d, 7e and 7g). I found it. Under the same experimental conditions, preimmune serum did not stain synaptonemal structures (FIGS. 7b and 7c). M118 anti-BRCA1 antibody stained unpaired chromosomes in mouse thick and double thread spermatocytes (FIGS. 7f and 7h). FANCD2 Ab staining of the non-synaptic axis of the sex chromosome was interrupted, showing a beaded appearance (Fig. 7g). Serial testing of 20 mitotic nuclei shows that the majority (~ 65%) of these anti-FANCD2 foci co-localize with regions of intense anti-BRCA1 staining and further support the interaction between these proteins (FIGS. 7g, 7h, and 7i). These results provide the first example of a FANC protein (activated FANCD2) that binds to chromatin.

Example 9: Experimental protocol Northern hybridization for obtaining and analyzing DNA and protein sequences for FANCD2 . Human adult and fetal multiple tissue mRNA blots were purchased from Clontech (Palo Alto, Calif.). The blot was investigated using 32P labeled DNA from EST clone SGC34603. Standard hybridization and wash conditions were used. Equivalent loading was confirmed by rehybridizing the blot with an actin cDNA probe.

  Mutation analysis. Total cellular RNA was reverse transcribed using a commercial kit (Gibco / BRL). The 5 'end portion of FANCD2 was amplified from the resulting patient and control cDNAs using a nested PCR protocol. The first round was performed with primers (SEQ ID NO: 97) MG471 5'-AATCGAAAACTACGGGG-3 'and (SEQ ID NO: 98) MG457 5'-GAGAACACATGAATGAACGC-3'. The PCR product from this round was diluted 1:50 for the next round with primers (SEQ ID NO: 99) MG492 5′-GGCGGACGGCTCTCCGGAAGTAATTTAAG-3 ′ and (SEQ ID NO: 100) MG472 5′-AGCGGCAGGAGGTTTATG-3 ′ did. PCR conditions were as follows: 94 ° C. for 3 minutes, followed by 25 cycles of 94 ° C. for 45 seconds, 50 ° C. for 45 seconds, 72 ° C. for 3 minutes and finally 72 ° C. for 5 minutes. The 3 'portion of this gene was amplified as described above except that the primers (SEQ ID NO: 101) MG474 5'-TGGCCGCAGACAGAAGTG-3' and (SEQ ID NO: 102) MG475 5'-TGGGCGCAGACAGAAGTG-3 'were used. The second round was performed with (SEQ ID NO: 103) MG491 5'-AGAGAGCCAACCTGAGCGGATG-3 'and (SEQ ID NO: 104) MG476 5'-GTGCCCAGACTCTGGTGGG-3'. PCR products were gel purified, cloned into the pT-Adv vector (Clontech) and sequenced using internal primers.

  Allele specific assay. Allele-specific assays were performed in the PD20 family and 290 control samples (= 580 chromosomes). The PD20 family is a mixed Nordic family, and VU008 is a Dutch family. Control DNA samples were samples from unrelated individuals in the CEPH family (n = 95), samples from unrelated North American families, either ectodermal dysplasia (n = 95) or Fanconi anemia (n = 94). It was. This maternal nt376a → g mutation in the PD20 family created a novel MspI restriction site. For genomic DNA, this assay uses a primer located in exon 4 (SEQ ID NO: 105) MG792 5′-AGGAGACACCCTTCCTATCC-3 ′ and a primer in intron 5 (SEQ ID NO: 106) M0803 5′-GAAGTTGGCAAAACAGACTTG-3 ′ And amplifying the genomic DNA. The size of the PCR product was 340 bp, and when the mutation was present, two fragments, 283 bp and 57 bp, were produced after MspI digestion. To analyze the backmutated cDNA clones, PCR was performed using primers (SEQ ID NO: 107) MG924 5'-TGTCTTGTTGAGCGTCTGCAGG-3 'and (SEQ ID NO: 108) MG753 5'-AGGTTTGATAATGGCAGGGC-3'. The paternal exon 37 mutation (R1236H) in PD20 and the exon 12 missense mutation (R302W) in VU008 were tested by allele-specific oligonucleotide (ASO) hybridization (Wu et al., DNA, (1989), vol. 8). , P135-142). For the exon 12 assay, genomic DNA was amplified using primers (SEQ ID NO: 109) MG979 5'-ACTGGACTGTGCCCACCACCACTTG-3 'and (SEQ ID NO: 110) MG984 5'-CCTGTGTGGAGATGAGCTCT-3'. For exon 37, primers (SEQ ID NO: 171) MG818 5'-AGAGGTTAGGAGAGAGACTAC-3 'and (SEQ ID NO: 172) MG813 5'-CCAAAGTCCCACTTCTTGAAG-3' were used. Wild type (SEQ ID NO: 111) (5′-TTCTCCCCAGAGCTCAG-3 ′ for R302W and (SEQ ID NO: 112) 5′-TTTCTCCCGTGTGATGA-3 ′) for R302W and mutant (SEQ ID NO: 111) ( For R302W 5′-TTCTCCCAAAGCTGAG-3 ′ and for R1236H (SEQ ID NO: 112) 5′-TYTCTCTCGTTGATGA-3 ′) Oligonucleotides were end-labelled with γ32P- [ATP] and previously described Hybridized to the target PCR product dot blotted as a new DdeI site. The wild type PCR product is digested into 117 and 71 bp products, while the mutant allele produces three fragments of length 56, 61 and 71 bp. PCR in all of the above assays was performed with 50 ng genomic DNA for 37 cycles consisting of 94 ° C. for 25 seconds, 50 ° C. for 25 seconds and 72 ° C. for 35 seconds.

  Generation of anti-FANCD2 antiserum. Rabbit polyclonal antisera against FANCD2 was generated using GST-FANCD2 (N-terminal) fusion protein as the antigen source. The 5 ′ fragment was linked to the full length of the cDNA using the primers (SEQ ID NO: 113) DF4EcoRJ (5′-AGCCTCgaattcGUTCCAAAAAGAAGACTGTCA-3 ′) and (SEQ ID NO: 114) DR816Xh (5′-GGTATCctcgagTCAAGAGAGAACTACTATTCCATCA-3 ′) to the full length of cDNA from FA PCR). The resulting 841 bp PCR product encoding the amino terminal 272 amino acids of the FANCD2 polypeptide was digested with EcoRI / XhoI and subcloned into the EcoRI / XhoI site of plasmid pGEX4T-1 (Pharmacia). A GST-FANCD2 (N-terminal) fusion protein of expected size (54 kD) was expressed in E. coli strain DH5, purified with glutathione-S-Sepharose, and used to immunize New Zealand white rabbits. The FANCD2-specific immune antiserum was affinity purified by passing through an AminoLink Plus column (Pierce) loaded with GST protein and through an AminoLink Plus column loaded with GST-FANCD2 (N-terminal) fusion protein.

  Immunoblotting is as described in Example 1.

  Cell lines and transfection. PD20i is an immortalized FA fibroblast cell line and PD733 is a primary FA fibroblast cell line produced by the Oregon Health Sciences Fanconi anemia cell reservoir (Jakobs et al., Somat. Cell. Mol. Genet. , (1996), vol. 22, p151-157). PD20 lymphoblasts were derived from bone marrow samples. VU008 is a lymphoblast and VU423 is a fibroblast cell line produced by the European Fanconi Anemia Registry (EUFAR). VU423i was an immortalized cell line induced by transfection with SV40 T-antigen (Jakobs et al., 1996) and telomerase (Bodnar et al., Science, (1998), vol. 279, p349-352). . Other FA cell lines have been previously described. Human fibroblasts were cultured in MEM and 20% fetal calf serum. Transformed lymphoblasts were cultured in RPMI 1640 supplemented with 15% heat-inactivated fetal calf serum.

  To generate a FANCD2 expression construct, full length cDNA was constructed from the cloned RT-PCR product in pBluescript, and the absence of PCR-induced mutations was confirmed by sequencing. Expression vectors pIRES-Neo, pEGFP-Nl, pRevTRE and pRevTet-off were obtained from ClonTech (Palo Alto, Calif.). FANCD2 was inserted into the appropriate multicloning site of these vectors. The expression construct was electroporated into cell line PD20 and normal control fibroblast line GM639 using standard conditions (van den Hoff et al., 1992). Neomycin selection was performed with 400 μg / mL active G418 (Gibco).

Whole cell fusion. For whole cell fusion studies, the PD20 cell line (PD20i) that is resistant to hygromycin B and lacks the HPRT locus was used (Jakobs et al., Somat. Cell. Mol. Genet., (1997). , Vol.23, p1-7). Controls included PD24 (primary fibroblasts from sister cells infected with PD20) and PD319i (Jakobs et al., 1997) (immortalized fibroblasts from non-A, C, D or G type FA patients). 2.5 × 10 ⁵ cells from each cell line were mixed in a T25 flask and allowed to recover for 24 hours. Cells were washed with serum free medium and then fused with 50% PEG for 1 minute. After removal of PEG, cells were washed 3 times with serum-free medium and allowed to recover overnight in complete medium without selection. The next day, cells were split 1:10 in selective medium containing 400 μg / mL hygromycin B (Roche Molecular) and 1 × HAT. After selection was complete, the hybrids were cultured once and then analyzed as described below.

  Retroviral transduction and complementation analysis of FA-D2 cells. Full length FANCD2 cDNA was subcloned into the vector pMMP-puro (Pulsipher et al., 1998). Retrovirus supernatant was used to transduce PD20F and puromycin resistant cells were selected. Cells were analyzed for MMC sensitivity by crystal violet assay (Naf et al., 1998).

  Analysis of chromosome breaks. Analysis of chromosome breaks was performed by Cytogenetics Core Lab at OHSU (Portland, Oregon). For analysis (Cohen et al., 1982), cells were plated in T25 flasks, allowed to recover and then treated with 300 ng / mL DEB for 2 days. After treatment, cells were exposed to colcemid for 3 hours and harvested using 0.075 M KCl and 3: 1 methanol: acetic acid. Slides were stained with Wright stain and scored 50-100 metaphase (for mitosis) for radial.

Example 10: Mouse model for FA to be used in screening potential therapeutics A mouse model of FANCD2 is D'Andrea et al., (1997) 90: 1725-1736 and Yang et al., Blood, (2001) vol. 98, p1-6, can be made using homologous recombination or targeted disruption in embryonic stem cells. Knockout of the FANCD2 locus in mice is not a lethal mutation. These knockout animals have increased susceptibility to cancer and also exhibit other symptoms characteristic of FA. Administration of certain therapeutic agents to knockout mice is expected to reduce their sensitivity to cancer. In addition, it is expected that certain established chemotherapeutic drugs that are more effective for treating knockout mice that have developed cancer as a result of certain genetic defects will be identified, which have susceptibility to cancer, or It may also be useful in treating human subjects who have developed cancer as a result of mutations at the FANCD2 locus.

  For example, for FANCC, Chen et al., Nat. Genet. , (1996), vol. 12, p448-451, and Whitney et al. (1996), vol. 88, p49-58, can be used to create experimental mouse models with targeted disruption of FANCD2. In both animal models, spontaneous chromosome breaks in splenic lymphocytes and an increase in chromosome breaks are observed in response to bifunctional alkylating agents. In both models, FANCD2 − / − mice have germline defects and reduced fertility. The FANCD2 mouse knockout model consists of (1) the role of the FANCD2 gene in the physiological response of hematopoietic cells to DNA damage, (2) the in vivo effects of inhibitory cytokines on FA bone marrow cells, and (3) the effectiveness of gene therapy Useful in testing sex and (4) for screening candidate therapeutic molecules.

  The availability of other FA gene disruptions will allow the generation and characterization of mice using multiple FA gene knockouts. For example, if two FA genes function exclusively in the same cellular pathway, the double knockout should have the same phenotype as the single FA gene knockout.

  The mouse FANCD2 gene can be disrupted by replacing exons with a neomycin cassette flanked by FRT via homologous recombination in 129 / SvJae embryonic stem cells. Mouse homozygotes for FANCD2 mutations within a mixed genetic background of 129 / Sv and C57BL can be generated according to standard protocols. Mouse tail genomic DNA can be prepared as previously described and can be used as a template for genotyping by polymerase chain reaction (PCR).

  Splenocytes can be prepared from 6 week old mice of known FANCD2 genotype. The spleen was dissected and crushed in RPMI medium to give a single cell suspension and filtered through a 70 μm filter. Red blood cells were lysed in hypotonic ammonium chloride. The remaining splenic lymphocytes were washed in phosphate buffered saline and resuspended in RPMI / 10% fetal calf serum + phytohemagglutinin. Cells were tested for viability by trypan blue dye exclusion test. Cells were cultured in medium for 24 hours and exposed to MMC or DEB for an additional 48 hours. Alternatively, cells were cultured for 50 hours, exposed to IR (2 or 4 Gy as indicated) and allowed to recover for 12 hours prior to chromosome breakage or trypan blue dye exclusion test (viability) analysis.

Mononuclear cells can be isolated from the femur and tibia of 4-6 week old FANCD2 +/− or FANCD2 − / − mice, as previously described. A total of 2 × 10 ⁴ cells were cultured in 1 mL MethoCult M343 medium (StemCell Technologies, Vancouver, British Columbia) with or without MMC treatment. Colonies were scored on day 7, with the majority of colonies belonging to granulocyte-macrophage colony forming unit or erythroid burst forming unit lines. Each number was averaged from two plates and data was drawn from two independent experiments.

  Lymphocytes isolated from thymus, spleen, and peripheral lymph nodes are fluorescein isothiocyanate-conjugated anti-CD3, CD4, and CD19 and PE-conjugated anti-CD8, CD44, CD45B, immunoglobulin M, and B220 (BD PharMingen, CA) ) Was used to stain for T lymphocytes or B lymphocyte surface molecules. Stained cells were analyzed on a Counter Epis XL flow cytometry system.

  Mouse ovaries and testis were isolated and fixed in 4% paraformaldehyde and further processed at the central facility of the Department of Pathology, Massachusetts General Hospital.

Example 11: Screening assay using antibody reagents to detect increased cancer susceptibility in human subjects To test for the relative amount of FANCD2-S compared to FANCD2-L and the presence or absence of FANCD2-L A blood sample or tissue sample can be taken from the subject. Using antibody reagents specific for FANCD2-S protein and FANCD2-L protein (Example 1), positive samples can be identified by Western blotting as shown in FIG. Other antibody assays such as the one-step migration binding band assay described in, for example, 5,654,162 and 5,073,484 can be utilized. Enzyme immunoassays (ELISA), sandwich assays, radioimmunoassays and other immunodiagnostic assays known in the art can be used to determine the relative binding concentrations of FANCD2-S and FANCD2-L.

The feasibility of this approach is explained by the following:
FANCD2 Diagnostic Western Blot for Screening Human Cancer Cell Lines Human cancer cell lines are treated with or without ionizing radiation (as shown in FIG. 14), total cell proteins are electrophoresed, and nitro Transfer to cellulose and immunoblotting using the anti-FANCD2 monoclonal antibody of Example 1. The ovarian cancer cell line (TOV21G) expressed FANCD2-S but not FANCD2-L (see lanes 9 and 10). This cell line has a deletion of human chromosome 3p that overlaps the FANCD2 gene, is hemizygous for FANCD2, and has a mutation in the second FANCD2 allele, It is expected that the second FANCD2 allele cannot be monoubiquitinated by the PA complex and therefore does not have FANCD2-L (lanes 9, 10). This example demonstrates that antibody-based tests are suitable for measuring damage in the FANCD2 gene that causes increased cancer susceptibility.

Example 12 Screening Assay Using Nucleic Acid Reagents to Detect Increased Cancer Susceptibility in Human Subjects To determine the size and location of genetic lesions when present in the genome of a subject, a blood or tissue sample is It can be taken from a subject and screened using sequencing techniques or nucleic acid probes. This screening method may include sequencing the entire gene or using a probe set or a single probe to identify a lesion. Single lesions can be dominant in the population, but other lesions occur at low frequency throughout the gene, as in other genetic conditions such as cystic fibrosis and the P53 tumor suppressor gene. It is expected to be possible.

The feasibility of this approach is explained by the following:
Peripheral blood lymphocytes are isolated from the patient using the Ficoll-Hypaque gradient method and genomic DNA is isolated from these lymphocytes. We use genomic PCR to amplify 44 exons of the human FANCD2 gene (see Table 7 of primers) and sequence the two FANCD2 alleles to identify mutations. When such mutations were found, we distinguished them from benign polymorphisms by their ability to remove the functional complementation of the FA-D2 indicator cell line.

Example 13: Measurement of monoubiquitinated FANCD2-L in biopsy tissue Biopsy tissue was obtained by needle aspiration or skin puncture biopsy. Cells resuspended in the appropriate culture medium in the microtiter plate are then transferred to the indicated concentrations of MMC (0, 10, 40, 160 ng / mL) or indicated doses of IR (0, 5, 10, 10). , 20 Gy). After 24 hours incubation with MMC, or 2 hours after IR treatment, whole cell extracts were protease inhibitors (1 μg / mL leupeptin and pepstatin, 2 μg / mL aprotinin, 1 mM phenylmethylsulfonyl fluoride). And lysis buffer (50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1% (v / v) Triton X-100) supplemented with phosphatase inhibitor (1 mM sodium orthovanadate, 10 mM sodium fluoride) ). Thereafter, as disclosed herein, using anti-FANCD2-L specific monoclonal antibodies and conventional immunoassays such as enzyme immunoassays (ELISA) commonly used to quantify protein levels in cell samples The samples were then tested for the presence of the FANCD2-L isoform (Harlow, E. and Lane, D., “Use of Antibodies: A Laboratory Manual” (1999) Cold Spring Harbor Laboratory). ).

Example 14: Diagnosis of a cancer-related defect in Fanconi anemia / BRCA gene or protein
PCR amplification and sequencing of human FANCD2 gene-cDNA and genomic DNA templates
Genomic DNA Sequencing While sequencing the FANCD2 gene, it was found that there are at least 8 pseudogene sequences for FANCD2 in the human genome, all of which are located on human chromosome 3p (attached) See Table 8). Therefore, it was important to design a specific genomic PCR assay designed to specifically amplify the FANCD2 sequence and eliminate pseudogenes. Exons 1, 2, 3, 7-14, 19-22, 23-29, 30-32, 33-36 and 43- to functional FANCD2 gene that also does not amplify one or more non-functional copies of those exons It was impossible to design a PCR primer close to 44. First generate large PCR products unique to these regions of the functional gene, and then use them as templates in subsequent amplification reactions to generate exon PCR products using primers that are not specific to the functional gene. By using unique products, extremely excess PCR products were generated from functional genes that exceeded the PCR products from those copies. This method made it possible to detect mutations in functional genes.

Super amplicon PCR
As pointed out above, the purpose of these PCR reactions is to generate large amplicons (superamplicons) that are unique to certain regions of the functional FANCD2 gene. Components of the PCR were as follows: _Tris-S0 4 (pH8.9) of _{60mM, (NH 4) 2 SO} 4 in 18 mM, of 2.0 mM MgSO _4, each 0.2mM of dATP, dCTP, dGTP, TTP, 0.1 μM each primer, 5 ng / μL DNA, 0.05 units / μL Platinum Taq DNA Polymerase High Fidelity (GIBCO BRL, Gaithersburg, MD).

  Thermal cycling conditions were as follows: 94 ° C. for 4 minutes; each cycle followed by a denaturation step at 94 ° C. for 20 seconds and an extension step at 72 ° C. for 300 seconds, and the first cycle started at 64 ° C. 11 cycles including an annealing step of 20 seconds that reduces the temperature at 1 ° C / cycle to decrease to 54 ° C in the 11th cycle; then the 11th cycle was repeated 25 times; incubated at 72 ° C for 6 minutes, The program was then completed by immersion at 4 ° C.

Primer identity was as follows (primer sequences are shown in Table 9):

Exon PCR
There are two types of these PCRs: (1) Superamplicon PCR is used as a DNA template: 1-3, 7-14, 19-22, 23-29, 30-32, 33-36 and 43 ~ 44 are included in this group, and (2) unamplified genomic DNA is used as a DNA template; exons 4-6, 15-18 and 37-42 are included in this group.

  One primer in each pair (designated “−F”) was synthesized using an 18 base M13-21 forward sequence (TGTAAAACGACGGCGCAGT) at its 5 ′ end and another primer (designated “−R”). ) Was synthesized using an M13-28 reverse sequence (CAGGAAACAGCTATGACC) of 18 bases at its 5 ′ end. For exon 15, two overlapping amplicons were designed.

Components of the PCR reaction solution 10μL is as follows: 20 mM of Tris-HCl (pH8.4), 50mM of KCl, MgCl ₂ of 1.5 mM, each of 0.1mM dATP, dCTP, dGTP, TTP , 0.1 μM of each primer, 1 μL of either 1: 100 dilution of superamplicon PCR or 5 ng / μL of unamplified genomic DNA, 0.05 units / μL Taq polymerase (Taq Platinum, GIBCO BRL, Gaithersburg, Mary Land). Thermal cycling conditions are as follows: 94 ° C. for 4 minutes; each cycle followed by a denaturation step at 94 ° C. for 30 seconds and an extension step at 72 ° C. for 20 seconds, and the first cycle starting at 60 ° C. Eleventh cycle with an annealing step of 20 seconds that reduces the temperature at 1 ° C / cycle to decrease to 50 ° C in the eleventh cycle; then the eleventh cycle was repeated 25 times; incubated at 72 ° C for 6 minutes, then The program was completed by immersion at 4 ° C.

cDNA Sequencing 2 μg of total RNA was converted to cDNA using Superscript First-Strand Synthesis System (GIBCO / BRL) for RT-PCR according to manufacturer's instructions. One-twentieth of the RT-PCR reaction was used as a DNA template in each of the 18 PCR reactions; these PCR reactions amplify the coding region of the cDNA in overlapping fragments. Primers are shown in the table below.

  One primer in each pair (designated “−F”) was synthesized using an 18 base M13-21 forward sequence (TGTAAAACGACGGCGCAGT) at its 5 ′ end and another primer (designated “−R”). ) Was synthesized using an M13-28 reverse sequence (CAGGAAACAGCTATGACC) of 18 bases at its 5 ′ end.

Components of the PCR reaction solution 10μL is as follows: 20 mM of Tris-HCl (pH8.4), 50mM of KCl, MgCl ₂ of 1.5 mM, each of 0.1mM dATP, dCTP, dGTP, TTP , 0.1 μM of each primer, 1 μL of either 1: 100 dilution of superamplicon PCR or 5 ng / μL of unamplified genomic DNA, 0.05 units / μL Taq polymerase (Taq Platinum, GIBCO BRL, Gaithersburg, Mary Land).

The thermal cycling conditions are as follows: 94 ° C. for 4 minutes, each cycle followed by a denaturation step at 94 ° C. for 30 seconds and an extension step at 72 ° C. for 20 seconds, and the first cycle starting at 60 ° C. Eleventh cycle with an annealing step of 20 seconds that reduces the temperature at 1 ° C / cycle to decrease to 50 ° C in the eleventh cycle; then the eleventh cycle was repeated 25 times; incubated at 72 ° C for 6 minutes, then The program was completed by immersion at 4 ° C.

DNA sequencing Each PCR reaction aliquot was diluted 1:10 with water. Diluted PCR products were sequenced on both strands using M13 forward and M13 reverse Big Dye primer kits (Applied Biosystems, Foster City, Calif.) According to manufacturer's recommendations. Sequencing products were separated on a fluorescent sequencer (model 377, Applied Biosystems, Foster City, CA). The base call was made with equipment software and examined by visual inspection. Each sequence was compared to the corresponding normal sequence using Sequencher 3.0 software (LifeCodes).

Example 15: Chemosensitizer screening method As shown in the FA / BRCA pathway model, the enzyme monoubiquitination of FANCD2 is an important regulatory event. This event requires an intact FA protein complex (A / C / E / F / G complex) and requires BRCA1 and BRCA2. Although the actual catalytic subunit required for FANCD2 monoubiquitination remains unknown, it is still possible to screen for antagonists of monoubiquitination. As described elsewhere herein, for the most part, inhibitors of the FA pathway can function as chemosensitizers for cisplatin in the treatment of ovarian cancer or other cancers. Screening for inhibitors of FANCD2 monoubiquitination can be performed as a simple mammalian cell-based screen. Mammalian tissue culture cell lines, such as HeLa cells, are first pre-incubated with random candidate small molecules. Cell clones are then screened using anti-FANCD2 Western blot. Inhibitors (antagonists) of the FA pathway block FANCD2 monoubiquitination.

  As described in Garcia-Higuera et al., 2001, BRCA1 may actually be an enzyme that monoubiquitinates FANCD2. Accordingly, BRCA1 has a ubiquitin ligase (Ring Finger) catalytic domain. For this reason, an in vitro assay is devised to screen for BRCA1-mediated monoubiquitination of FANCD2. Inhibitors are screened directly for the ability to inhibit this in vitro reaction. Once inhibitors are identified, such agents can be used to determine their function as cisplatin sensitizers in animal or phase 1 human studies.

Example 16: Screening method for potential cancer therapeutics Cells and animals with Fanconi anemia / BRCA pathway genes with one or more cancer-related defects can be studied and tested for potential therapeutic agents. Can be used as a model system. The cell is typically a cultured epithelial cell. These can be isolated from individuals with a Fanconi anemia / BRCA pathway gene that has one or more cancer-related defects and are either somatic or germline. Alternatively, a cell line with a mutation in a Fanconi anemia / BRCA pathway gene having one or more cancer-related defects can be engineered.

  After the test substance is applied to the cells, the phenotype of the cells transformed by the tumor is determined. Any trait of cells transformed by the tumor can be assessed, including anchorage independent growth, tumorigenicity in nude mice, cell invasiveness, and growth factor dependence. Assays for each of these traits are known in the art.

  Animals for testing therapeutic agents can be selected after mutagenesis of all animals or after treatment of germline cells or conjugates. Such treatment includes the insertion of a mutant Fanconi anemia / BRCA pathway gene, usually having one or more cancer-related defects from a second animal species, as well as the insertion of a disrupted homologous gene. Alternatively, the animal's endogenous Fanconi anemia / BRCA pathway gene can be disrupted by insertion or deletion mutations or other genetic changes using conventional techniques, as outlined in Example 10 ( Capecchi, 1989; Valancius and Smithies, 1991; Hasty et al., 1991; Shinkai et al., 1992; Mambaerts et al., 1992; Philpott et al., 1992; Snowwaert et al., 1992; After the test substance is administered to the animals, tumor growth must be assessed. Where the test substance prevents or inhibits tumor growth, the test substance is a candidate therapeutic for treating the cancer identified herein.

Example 17: Method for treating cancer resistant to antitumor agents This example describes the treatment of patients with cancer resistant to antitumor agents such as cisplatin. This protocol provides for administration of cisplatin as described herein in combination with increasing doses of an inhibitor of FANCD2 protein ubiquitination as a chemosensitizer. Cisplatin and chemosensitizers can be administered intravenously, subcutaneously, intratumorally or intraperitoneally. The physician administering the drug can adjust the dose and timing of the drug based on the results observed using standard measures of cancer activity known in the art. Inhibition of tumor growth and metastasis represents an effective treatment for cancer.

Example 18: Method for Measuring Future Effectiveness of Therapeutic Agents Biopsy tissue of tumors from cancer patients being treated with therapeutic agents was obtained by needle aspiration or skin puncture biopsy. Cells resuspended in the appropriate culture medium in the microtiter plate are then transferred to the indicated concentrations of MMC (0, 10, 40, 160 ng / mL) or indicated doses of IR (0, 5, 10, 10). , 20 Gy). After 24 hours incubation with MMC, or 2 hours after IR treatment, whole cell extracts were protease inhibitors (1 μg / mL leupeptin and pepstatin, 2 μg / mL aprotinin, 1 mM phenylmethylsulfonyl fluoride). And phosphatase inhibitor (1 mM sodium orthovanadate, 10 mM sodium fluoride) added lysis buffer (50 mM Tris-HCl (pH 7.4), 150 mM NaCl, 1% (v / v) Triton X-100) Prepared in. Thereafter, as disclosed herein, using anti-FANCD2-L specific monoclonal antibodies and conventional immunoassays such as enzyme immunoassays (ELISA) commonly used to quantify protein levels in cell samples The samples were then tested for the presence of the FANCD2-L isoform (Harlow, E. and Lane, D., “Use of Antibodies: A Laboratory Manual” (1999) Cold Spring Harbor Laboratory). ). Detection of monoubiquitinated FANCD2-L isoforms is thought to indicate a decrease in the effectiveness of therapeutic agents used to treat cancer patients.

Example 19: Method for Determining Resistance to Chemotherapeutic A flow chart describing the protocol used to determine the methylation status of Fanconi anemia / BRCA pathway genes is shown in FIG.

Analysis of FANCF methylation The DNA methylation pattern in the FANCF gene was determined by methylation-specific PCR or a PCR-based HpaII restriction enzyme assay. Genomic DNA was isolated from the indicated cell lines using the QIAamp DNA blood mini kit (QIAGEN).

PCR-based HpaII restriction enzyme assay 250 ng of genomic DNA was digested with 30 units of HpaII or MspI at 37 ° C. for 12 hours. 12.5 ng of DNA from each digest contains 1 × PCR buffer, 200 μM each of 4 deoxynucleotide triphosphates, 0.5 units of AmpliTaq DNA polymerase (Roche), and 0.2 μM of each primer Analyzed by PCR in 10 μL reaction. PCR was performed for 33 cycles, each cycle being denaturing (94 ° C. for 45 seconds, first cycle 4 minutes 45 seconds), annealing (61 ° C. for 1 minute), and extension (72 ° C. for 2 minutes, final cycle 9 Minutes). The PCR reaction was electrophoresed on a 1.2% agarose gel containing ethidium bromide. The primers used were FPF6 (5′-GCACCCTCATGGAATCCCTTC-3 ′) (forward) and FR343 (5′-GTTGCTGCACCAGGGTGTAA-3 ′) (reverse). These primers were designed using nt-6-14 for the forward primer and nt 403-432 for the reverse primer.

Methylation specific PCR
Bisulfite modification of genomic DNA was performed as previously described (Herman JG et al., Proc Natl Acad Sci USA 93 (18), 9821-6 (1996)). Bisulfite treated DNA was amplified using either methylation specific or unmethylation specific primer sets. PCR was performed for 40 cycles, each cycle being denaturing (94 ° C. for 45 seconds, first cycle 4 minutes 45 seconds), annealing (65 ° C. for 1 minute), and extension (72 ° C. for 2 minutes, final cycle 9 Minutes). The PCR reaction was electrophoresed on a 3% Separide (Gibco) gel containing ethidium bromide. The methylation specific primers were FF280M (5′-TTTTTGCGGTTTGTTGGAGAATCGGGTTTTC-3 ′) (forward) and FR432M (5′-ATACACCGCAAACGCCGCGACGAACAAAACG-3 ′) (reverse). The unmethylated specific primers were FF280U (5'-TTTTTGTGTTTGTTGGGAGAATTGGGTTTTT-3 ') (forward) and FR432U (5'-ATACACCCACAAACCACCCAACAAAAAAAACA-3') (reverse). These primers were designed using nt 280-309 for the forward primer and nt 403-432 for the reverse primer.

All patents, patent applications, and publications cited herein are hereby incorporated by reference in their entirety. While the invention has been particularly shown and described with reference to preferred embodiments thereof, those skilled in the art will recognize that various forms and details can be made without departing from the scope of the invention as encompassed by the appended claims. It will be understood that it can be varied.

  The foregoing features of the invention will be more readily understood by reference to the detailed description taken in conjunction with the accompanying drawings.

FIG. 1A is a Western blot showing that the Fanconi anemia protein complex is required for monoubiquitination of FANCD2. Normal (WT) cells (lane 1) express two isoforms of the FANCD2 protein, a low molecular weight isoform (FANCD2-S) (155 kD) and a high molecular weight isoform (FANCD2-L) (162 kD). Lanes 3, 7, 9, and 11 show that FA cell lines derived from type A, C, G, and F patients express only the FANCD2-S isoform. Lanes 4, 8, 10, 12 show the recovery of the high molecular weight isoform FANCD2-L after transfection of the cell line with the corresponding FA cDNA.

  FIG. 1B shows a Western blot obtained after transfection of HeLa cells with cDNA encoding HA-ubiquitin. After transfection, the cells were treated with the indicated amount of mitomycin C (MMC). Cellular proteins were immunoprecipitated using a polyclonal antibody against FANCD2 (E35) as indicated. FANCD2 was immunoprecipitated and immune complexes were blotted using anti-FANCD2 or anti-HA monoclonal antibodies.

  FIG. 1C shows a Western blot obtained after transfection of HeLa cells with cDNA encoding HA-ubiquitin. Following transfection, the cells were treated with the indicated dose of ionizing radiation (IR). FANCD2 was immunoprecipitated and immune complexes were blotted using anti-FANCD2 or anti-HA monoclonal antibodies.

  FIG. 1D shows that FANCD2 was immunoprecipitated after anti-FANCD2 or anti-HA antiserum was transfected after transfecting PA-G fibroblast cell line (FAG326SV) or corrected cells (FAG326SV + FANCG cDNA) with HA-Ub cDNA. And blotted.

FIG. 1E shows a Western blot obtained after treatment of HeLa cells with 1 mM hydroxyurea for 24 hours. HeLa cell lysates were extracted and incubated at the indicated temperatures for the indicated times with or without 2.5 μM ubiquitin aldehyde. FANCD2 protein was detected by immunoblotting using monoclonal anti-FANCD2 (F117).
FIG. 2 shows that the Fanconi anemia pathway is required to form the FANCD2 nuclear focus. The upper panel shows an anti-FANCD2 immunoblot of SV40 transformed fibroblasts prepared as a whole cell extract. Panels a to h show immunofluorescence using affinity purified anti-FANCD2 antiserum. Uncorrected (mutant, M) FA fibroblasts were FA-A (GM6914), FA-G (FAG326SV), FA-C (PD426), and FA-D (PD20F). FA-A, FA-G, and FA-C fibroblasts were functionally complemented with the corresponding FA cDNA. FA-D cells were complemented with neomycin-labeled human chromosome 3p (Whitney et al., 1995). FIG. 3 shows cell cycle-dependent expression of two isoforms of FANCD2 protein. (A) HeLa cells, SV40 transformed fibroblasts (GM6914) from FA-A patients, and GM6914 cells corrected with FANCA cDNA were synchronized by the double thymidine block method. Cells corresponding to the indicated phase of the cell cycle were lysed and processed for FANCD2 immunoblotting. (B) Synchronization with nocodazole block. (C) Synchronization with mimosine blocks. (D) HeLa cells were synchronized in the cell cycle using nocodazole or (e) mimosine, and cells corresponding to the indicated phase of the cell cycle were immunostained with anti-FANCD2 antibody and analyzed by immunofluorescence. FIG. 4 shows the formation of activated FANCD2 intranuclear focus after cell exposure to MMC, ionizing radiation, or ultraviolet light. Exponentially growing HeLa cells are either untreated or indicated DNA damaging agents (a) mitomycin C (MMC), (b) gamma irradiation (IR), or (c) ultraviolet (UV) ) And processed for FANCD2 immunoblotting or FANCD2 immunostaining. (A) Cells were continuously exposed to 40 ng / mL MMC for 0-72 hours as indicated or treated for 24 hours and fixed for immunofluorescence. (B) and (c) Cells are exposed to gamma rays (10 Gy, B) or UV rays (60 J / m ² , C) and collected after the indicated time (upper panel) or irradiated at the indicated dose. 1 hour later (lower panel). For immunofluorescence analysis, cells were fixed 8 hours after treatment (B, 10 Gy, C, 60 J / m ² ). (D) treating the indicated EBV transformed lymphoblastoid line from normal individuals (PD7) or from various Fanconi anemia patients continuously with 40 ng / mL mitomycin C (lanes 1-21), or Exposed to 15 Gy gamma rays (lanes 22-33) and processed for FANCD2 immunoblotting. Up-regulation of FANCD-L after MMC or IR treatment was seen in PD7 (lanes 2-5) and corrected FA-A cells (lanes 28-33), but in either mutant Fanconi anemia cell line Not observed. Similarly, IR-induced FANCD2 intranuclear focus was not detected in PA fibroblasts (FA-G + IR) but recovered after functional complementation (PA-G + FANCG). FIG. 5 shows the co-localization of activated FANCD2 and BRCA1 in discrete nuclear foci after DNA damage. HeLa cells were either untreated or exposed to ionizing radiation (10 Gy) as indicated and fixed after 8 hours. (A) Cells are double-stained with D-9 monoclonal anti-BRCA1 antibody (green, panels a, d, g, h) and rabbit polyclonal anti-FANCD2 antibody (red, panels b, e, h, k), Stained cells were analyzed by immunofluorescence. When the green and red signals overlap (Merge, panels c, f, i, l), a yellow pattern is seen, representing colocalization of BRCA1 and FANCD2. (B) Co-immunoprecipitation of FANCD2 and BRCA1. HeLa cells were either untreated (-IR) or exposed to 15 Gy gamma irradiation (+ IR) and harvested after 12 hours. Cell lysates were prepared and either monoclonal FANCD2 antibody (FI-17, lanes 9-10) or any one of the three independently obtained monoclonal antibodies against human BRCA1 (lanes 3-8) Were immunoprecipitated using: D-9 (Santa Cruz), Ab-1 and Ab-3 (Oncogene Research Products). The same amount of purified mouse IgG (Sigma) was used for the control sample (lanes 1-2). Immune complexes were separated by SDS-PAGE and immunoblotted with anti-FANCD2 or anti-BRCA1 antiserum. The FANCD-L isoform preferentially co-immunoprecipitated with BRCA1. FIG. 6 shows the co-localization of activated FANCD2 and BRCA1 at discrete nuclear focus during S phase. (A) HeLa cells were synchronized with mimosine in late G1 phase and released in S phase. S-phase cells were double-stained with a monoclonal anti-BRCA1 antibody (green, panels a, d) and a rabbit polyclonal anti-FANCD2 antibody (red, panels b, e), and the stained cells were analyzed by immunofluorescence. When the green and red signals overlap (merge, panels c, f), a yellow pattern is seen, representing colocalization of BRCA1 and FANCD2. (B) HeLa cells synchronized in S phase are either untreated (a, b, k, l) or, as indicated, IR (50 Gy, panels c, d, m, n), MMC (20 μg / ML, panels c, f, o, p), or UV (100 J / m ² , panels g, h, q, r)) and fixed after 1 hour. Subsequently, cells were immunostained with antibodies specific for FANCD2 or BRCA1. FIG. 7 shows that FANCD2 forms a focus on synaptonemal structures that can co-localize with BRCA1 during meiosis I in mouse spermatocytes. (A) Anti-SCP3 (white) and anti-FANCD2 (red) staining of the synaptonemal structure in the late mitotic mouse nucleus. (B) SCP3 staining of late mitotic chromosomes. (C) Staining of this smear with pre-immune serum against anti-FANCD2 E35 antibody. (D) Anti-SCP3 staining of synaptonemal structures in mouse bifilar nuclei. (E) Co-staining of this smear with E35 anti-FANCD2 antibody. Note the staining of both unpaired sex chromosomes and autosomal telomeres with anti-FANCD2. (F) Co-staining of this smear with anti-BRCA1 antibody. Sex chromosomes are preferentially stained. (G) Anti-FANCD2 staining of sex chromosome synaptonemal structure at late typhoid stage. (H) Anti-BRCA1 staining of the same complex. (I) Anti-FANCD2 (red) and anti-BRCA1 (green) co-staining (co-localization reflected by the yellow area). FIG. 8 is a schematic representation of FA protein interactions within the cellular pathway. FA proteins (A, C, and G) bind in a functional nuclear complex. When this complex is activated by either S phase progression or DNA damage, this complex enzymatically modifies (monoubiquitinates) the D protein. According to this model, activated D protein is subsequently targeted for nuclear focus, where it interacts with BRCA1 protein and other proteins involved in DNA repair. FIG. 9 shows heart, brain, placenta, liver, skeletal muscle, kidney, pancreas, spleen, thymus, prostate, testis, uterus, small intestine from a human adult, examined with full length FANCD2 cDNA and exposed for 24 hours. FIG. 5 shows Northern blots of cells from colon, peripheral blood lymphocytes and brain, lung, liver and kidney from human fetuses. FIG. 10 shows an allele-specific assay for mutation analysis of two FANCD2 families, with the family genealogy (a D) and panels b, c, e and f were arranged vertically. Panels a to c depict PD20, and panels df depict the VU008 family. Panels b and e show the separation of maternal mutations detected by the creation of a new MspI site (PD20) or DdeI site (VU008). Paternally inherited mutations in both families were detected using allele-specific oligonucleotide hybridization (panels c and f). FIG. 11 shows a Western blot analysis of FANCD2 protein in a human Fanconi anemia cell line. Whole cell lysates were generated from the indicated fibroblast and lymphoblast systems. Protein lysates (70 g) were examined directly by immunoblotting with anti-FANCD2 antiserum. FANCD2 proteins (155 kD and 162 kD) are indicated by arrows. Other bands in the immunoblot are nonspecific. (A) The cell lines tested included wild type cells (lanes 1 and 7), PD20 fibroblasts (lane 2), PD20 lymphoblasts (lane 4), revertant MMC resistant PD20 lymphoblasts (lanes). 5, 6), and chromosome 3P complement-binding PD20 fibroblasts (lane 3). Several other FA-D group cell lines were analyzed, including HSC62 (lane 8) and VU008 (lane 9). FA-A cells were HSC72 (lane 10), FA-C cells were PD4 (lane 11), and FA-G cells were EUFA316 (lane 12). (B) Identification of a third FANCD2 patient. The FANCD2 protein was easily detectable in wild type and FA-G group cells, but not in PD733 cells. (C) Specificity of the antibody. PD20i cells transduced with the retroviral FANCD2 expression vector displayed both FANCD2 protein isoforms, as opposed to empty vector control (lane 3) and untransfected PD20i cells (lane 2). (Lane 4). In wild type cells, the endogenous FANCD2 protein (two isoforms) was also immunoreactive with the antibody (lane 1). FIG. 12 shows functional complementation of FA-D2 cells using cloned FANCD2 cDNA. PD20i, an SV40 transformed FA-D2 fibroblast cell line, was transduced with pMMP-puro (PD20 + vector) or pMMP-FANCD2 (PD20 + FANCD2wt). MMC sensitivity analysis was performed on puromycin-selected cells. The analyzed cells were parent PD20F cells (Δ), PD20 (◯) corrected using human chromosome 3P, and either pMMP-puro (□) or pMMP-FANCD2 (wt) -puro (♦). Transduced PD20 cells. FIG. 13 shows the molecular basis for PD20 lymphoblast reversion. (A) PCR primers to exons 5 and 6 were used to amplify the cDNA. The control sample (right lane) produced a single band of 114 bp, while the PD20 cDNA (left lane) showed two bands, the larger band of 13 bp intron sequence into the maternal allele. Reflects the insertion. MMC resistant lymphoblasts back mutated from PD20 (middle lane) showed a third in-frame splice variant of 114 + 36 bp. (B) Schematic representation of splicing at the FANCD2 exon 5 / intron 5 boundary. In wild-type cDNA, 100% of splice events occur at the appropriate exon / intron boundary, whereas maternal A → G mutations (indicated by arrows) likewise result in abnormal splicing at 100%. In backmutated cells, all cDNAs with maternal mutations also have a second sequence change (thick arrow), either 13 bp (~ 40% mRNA) or 36 bp (~ 60% mRNA). A mixed splicing pattern with insertion was shown. FIG. 14 is a view showing a FANCD2 Western blot of a cancer cell line derived from an ovarian cancer patient. FIG. 15 is an alignment with flies and plant homologues using the sequence listing for the amino acid sequence of human FANCD2 and the BEAUTY algorithm (Worley et al., (1995), Genome Res., Vol. 5, p173-184). (SEQ ID NOs: 1-3) Black boxes indicate amino acid identity and gray boxes indicate similarity. The highest alignment score is D.E. Melanogaster (Drosophila melanogaster) (p = 8.4 × 10-58, accession number AAF55806) and A.I. It observed using the hypothetical protein in Tariana (Arabidopsis thaliana) (p = 9.4 * 10-45, accession number B71413). FIG. 16 is a diagram of the FANCD cDNA sequence 63-5127 nucleotides (SEQ ID NO: 5) and the polypeptide encoded by this sequence of amino acids 1-1472 (SEQ ID NO: 4). FIG. 17 shows FANCD-S. FIG. 7 is a nucleotide sequence diagram for the ORF (SEQ ID NO: 187). FIG. 18 is a diagram of a nucleotide sequence (SEQ ID NO: 6) for human FANCD2-L. FIG. 19 is a diagram of the nucleotide sequence (SEQ ID NO: 7) for human FANCD2-S. FIG. 20 is a diagram of the nucleotide sequence (SEQ ID NO: 8) for mouse FANCD2. FIG. 21 shows the protocol used to analyze the methylation status of the FANCF gene. FIG. 22 is a diagram showing the Fanconi anemia / BRCA pathway.

Claims (41)

  A method of diagnosing or determining whether a patient has cancer or whether the patient has an increased risk of developing cancer, said method comprising testing the Fanconi anemia / BRCA pathway gene for the presence of a cancer-related defect. And wherein the presence of the one or more cancer-related defects indicates an increase in cancer or cancer risk in the patient.   The method of claim 1, wherein the cancer is breast cancer, ovarian cancer, or prostate cancer.   The cancer-related defect results in a decrease in the ratio of FANCD2-L to FANCD2-S as compared to the ratio in patients who do not have one or more cancer-related defects in the Fanconi anemia / BRCA pathway gene. Item 2. The method according to Item 1.   A method of diagnosing or determining whether a patient has cancer or whether the patient has an increased risk of developing cancer, said method comprising testing a Fanconi anemia / BRCA pathway protein for the presence of a cancer-related defect. And wherein the presence of said cancer-related defect indicates an increase in cancer or cancer risk in said patient.   The method of claim 4, wherein the cancer is breast cancer, ovarian cancer, or prostate cancer. A method of diagnosing or determining whether a patient has an increased risk of carcinogenesis:
(A) providing a tissue sample from said patient;
(B) inducing DNA damage in cells of the tissue sample; and (c) assaying for the presence of FANCD2-S and FANCD2-L proteins in the cells;
Wherein a decrease in the ratio of FANCD2-L to FANCD2-S indicates an increased risk of developing cancer in said patient.   The method of claim 6, wherein the cancer is breast cancer, ovarian cancer, or prostate cancer.   7. The method of claim 6, wherein the patient does not have a known cancer-related defect in the BRCA-1 or BRCA-2 gene.   7. The method of claim 6, wherein the patient has one or more cancer-related defects in the BRCA-1 or BRCA-2 gene.   The method of claim 6, wherein a plurality of the tissue samples are distributed in an array. A method for determining whether a patient has cancer or whether the patient has an increased risk of carcinogenesis, wherein the patient has a known cancer that induces a defect in the BRCA-1 or BRCA-2 gene. Does not have the method:
(A) providing a DNA sample from the patient;
(B) amplifying the patient-derived FANCD2 gene using a FANCD2 gene-specific polynucleotide primer of SEQ ID NOs: 115-186;
(C) sequencing the amplified FANCD2 gene; and (d) comparing the FANCD2 gene sequence from said patient with a reference FANCD2 gene sequence, wherein a mismatch between the two gene sequences is indicative of a cancer-related defect. A step indicating existence;
Wherein the presence of one or more cancer-related defects indicates that the patient is cancerous or that the patient's risk of developing cancer is increased.   12. The method of claim 11, wherein the cancer is breast cancer, ovarian cancer, or prostate cancer.   12. The method of claim 11, wherein the patient does not have a known cancer-related defect in the BRCA-1 or FANC-D1 / BRCA-2 gene.   12. The method of claim 11, wherein the patient has one or more cancer-related defects in the BRCA-1 or FANC-D1 / BRCA-2 gene.   The method of claim 11, wherein a plurality of the DNA samples are distributed in a microarray. A method of screening for a chemosensitizer, said method comprising:
(A) providing a potential inhibitor of the Fanconi anemia / BRCA pathway;
(B) providing a tumor cell line that is resistant to one or more anti-tumor agents;
(C) contacting said tumor cell line and said potential inhibitor of Fanconi anemia / BRCA pathway and said one or more anti-tumor agents; and (d) said inhibitor of Fanconi anemia / BRCA pathway and said anti-tumor Measuring the growth rate of said tumor cell line in the presence of an agent;
A decrease in the growth rate of the tumor cell line relative to the cells of the tumor cell line in the presence of the anti-tumor agent and in the absence of the inhibitor of the Fanconi anemia / BRCA pathway is said potential inhibition A method for indicating that the agent is a chemical sensitizer.   The potential inhibitor of Fanconi anemia / BRCA pathway can be screened in a microarray, wherein the microarray contains an address containing one or more cells that are resistant to one or more anti-tumor agents. 16. The method according to 16.   17. The method of claim 16, wherein the potential inhibitor of Fanconi anemia / BRCA pathway is an inhibitor of FANCD2 protein ubiquitination.   The method according to claim 16, wherein the antitumor agent is cisplatin.   17. The method of claim 16, wherein the tumor cell line is an ovarian cancer cell line.   A method of treating a patient having cancer, wherein said cancer is resistant to an anti-tumor agent, said method comprising administering a therapeutically effective amount of a Fanconi anemia / BRCA pathway inhibitor together with said anti-tumor agent. Including methods.   The method of claim 21, wherein the antitumor agent is cisplatin.   24. The method of claim 21, wherein the potential inhibitor of Fanconi anemia / BRCA pathway is an inhibitor of FANCD2 protein ubiquitination.   24. The method of claim 21, wherein the tumor cell line is an ovarian cancer cell line. A method of screening for cancer therapeutics, said method comprising:
(A) providing one or more cells containing a Fanconi anemia / BRCA pathway gene having one or more cancer-related defects;
(B) growing the cells in the presence of a potential cancer therapeutic; and (c) the potential compared to the growth rate of equivalent cells grown in the absence of the potential cancer therapeutic. Determining the proliferation rate of the cells in the presence of a cancer therapeutic agent;
A decrease in the growth rate of the cells in the presence of the potential cancer therapeutic agent compared to the growth rate of equivalent cells grown in the absence of the potential cancer therapeutic agent. A method of indicating that the therapeutic agent is a cancer therapeutic agent.   27. The method of claim 26, wherein the cells containing a Fanconi anemia / BRCA pathway gene having one or more cancer-related defects are distributed in an array. A method for predicting the efficacy of a therapeutic agent in a cancer patient, said method comprising:
(A) providing a tissue sample from the cancer patient being treated with the therapeutic agent;
(B) inducing DNA damage in cells of the tissue sample;
(C) detecting the presence of FANCD2-L protein in the cell;
Wherein the presence of FANCD2-L represents reduced efficacy of the therapeutic agent in the cancer patient.   28. The method of claim 27, wherein the therapeutic agent is cisplatin. A method for determining resistance of tumor cells to an anti-tumor agent comprising:
(A) providing a tissue sample from a patient being treated with an anti-tumor agent;
(B) inducing DNA damage in cells of the tissue sample; and (c) measuring the methylation status of a Fanconi anemia / BRCA pathway gene;
Wherein methylation of the Fanconi anemia / BRCA pathway gene indicates tumor cell resistance to an anti-tumor agent.   30. The method of claim 29, wherein the Fanconi anemia / BRCA gene is a FANCF gene.   30. The method of claim 29, wherein the anti-tumor agent is cisplatin.   A kit for detecting a defect in the FANCD2 gene, comprising a polynucleotide primer pair specific for the FANCD2 gene, a reference FANCD2 gene sequence and packaging material therefor.   A kit for detecting the presence of FANCD2-L, comprising a FANCD2-L specific antibody and packaging material therefor.   A kit for measuring the methylation status of a Fanconi anemia / BRCA pathway gene, comprising a FANCD2 polynucleotide primer pair and probe, a control unmethylated standard FANCD2 gene sequence and packaging material therefor.   A kit for screening for a chemosensitizer, comprising a tumor cell line resistant to one or more anti-tumor agents and packaging material therefor.   36. The kit of claim 35, wherein the tumor cell line is an ovarian cancer cell line.   37. The kit of claim 36, wherein the ovarian cancer cell line is a cisplatin resistant ovarian cancer cell line.   The kit according to claim 36, wherein the antitumor agent is cisplatin.   A microarray containing one or more nucleic acid sequences from one or more Fanconi anemia / BRCA pathway genes.   40. The microarray of claim 39, wherein the gene is selected from the group consisting of ATM, FANCA, FANCB, FANCC, FANCD1, FANCD2, FANCE, FANCF and FANCG. A method for determining whether a patient has cancer or whether the patient has an increased risk of developing cancer, said method comprising:
(A) providing the microarray of claim 39;
(B) providing a nucleic acid sample from the patient;
(C) hybridizing the nucleic acid sample to the nucleic acid sequence from the Fanconi anemia / BRCA pathway in the microarray; and (d) the presence of a mutation in the Fanconi anemia / BRCA pathway gene in the nucleic acid sample from the patient. Detecting
Wherein the detection of the presence of the mutation indicates a patient with cancer or an increased risk of developing cancer.

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