US20170152565A1

US20170152565A1 - Method for diagnosing renal diseases or predispositions

Info

Publication number: US20170152565A1
Application number: US15/430,171
Authority: US
Inventors: Thomas C. Hart; Patricia Suzanne Hart; Michael Gorry; Anthony J. Bleyer
Original assignee: Wake Forest University; University of Pittsburgh
Current assignee: Wake Forest University; University of Pittsburgh
Priority date: 2002-10-23
Filing date: 2017-02-10
Publication date: 2017-06-01
Also published as: CA2501606A1; US20140243215A1; JP4546397B2; CA2501606C; JP2006503591A; AU2003301587A1; US20100285489A1; US20070207464A1; US9567638B2; US7781164B2; AU2003301587A8; WO2004038377A2; US8759001B2; WO2004038377A3

Abstract

The invention provides a method of diagnosing a disease or a predisposition to contract a disease by assaying for mutations of uromodulin (UMOD) within a test subject or patient. The presence of a mutation in the UMOD supports a diagnosis of a disease or a predisposition to contract a disease within the patient.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

This patent application is a continuation of Ser. No. 14/269,515, filed on May 5, 2014, which is a divisional of U.S. patent application Ser. No. 12/843,714, filed on Jul. 26, 2010, issued as U.S. Pat. No. 8,759,001 on Jun. 24, 2014, which is a continuation of U.S. patent application Ser. No. 11/112,327, filed on Apr. 23, 2005, issued as U.S. Pat. No. 7,781,164 on Aug. 24, 2010, which is a continuation-in-part of PCT/US03/33957, filed on Oct. 23, 2003, and claims the benefit of U.S. Provisional Patent Application No. 60/430,318, filed on Dec. 2, 2002, and U.S. Provisional Patent Application No. 60/420,768, filed on Oct. 23, 2002. The contents of each of these applications are incorporated herein in their entirety by reference thereto.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT

This invention was made in part with Government support under Grant Number DK62252 awarded by the National Institute of Diabetes and Digestive and Kidney Diseases. The United States Government may have certain rights in this invention.

INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED ELECTRONICALLY

Incorporated by reference in its entirety herein is a computer-readable nucleotide/amino acid sequence listing submitted concurrently herewith and identified as follows: One 89,394 bytes ASCII (Text) file named “727891_ST25.TXT,” created Feb. 10, 2017.

FIELD OF THE INVENTION

This invention pertains to methods and reagents for diagnosing diseases or a predisposition to develop a disease.

BACKGROUND OF THE INVENTION

Medullary cystic kidney disease 2 (i.e., “MCKD2,” Online Mendelian Inheritance in Man Ref. OMIN603860 (available on the Internet at: www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=603860) and familial juvenile gouty nephropathy (i.e., “FJGN” Online Mendelian Inheritance in Man Ref. OMIM162000 (available on the Internet at: www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=162000) are autosomal dominant renal diseases characterized by juvenile onset of hyperuricemia, gout, enuresis, and progressive renal failure. Both conditions typically result in death, unless renal trasnsplantation is preformed.
Because clinical features of both MCKD2 and FJGN vary in presence and severity, definitive diagnosis of both conditions is difficult before the onset of significant pathology. As such, currently, both conditions generally cannot be treated early, and prophylaxis typically is not possible for these conditions. Accordingly, there exists a need for a more sensitive diagnostic method and reagents for diagnosing diseases, such as MCKD2 and FJGN, or the predisposition to develop such diseases

BRIEF SUMMARY OF THE INVENTION

The invention provides a method of diagnosing a disease or a predisposition to contract a disease by assaying for mutations of uromodulin (UMOD, also known as Tamm-Horsfall glycoprotein (available on the Internet at: www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=191845) within a test subject or patient. The presence of a mutation in the UMOD supports a diagnosis of a disease or a predisposition to contract a disease within the patient.
The inventive method can permit diagnosis of diseases (e.g., MCKD2, FJGN, nephropathy, renal failure, hyperuricemia, gouty arthritis, enuresis, and the like) earlier than current methods, which can facilitate intervention and treatment of such diseases prior to the onset of significant pathology. In some applications, the method can identify a predisposition to develop such disorders even in a non-symptomatic patient. Furthermore, the method can be employed to screen a potential tissue donor or donated tissue or organs (e.g., a kidney or renal tissue) to minimize the risk to a transplant recipient of receiving donated tissue at risk for developing such disorders. These and other advantages of the invention, as well as additional inventive features, will be apparent from the description of the invention provided herein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A and 1B depict the pedigrees of families studied. Family 1: more than 300 individuals have been genealogically identified over 7 generations. The kindred is too large to include in total; thus, the nuclear families studied have been indicated for this report. These families are from different parts of this extended kindred, and are indicated as subfamilies A, B, C, and D. In addition eight singletons were studied. Clinical findings in affected family members are consistent with a clinical diagnosis of FJHN in Family 1. Family 2: Clinical findings in this family are consistent with a clinical diagnosis of FJHN. Family 3: Clinical findings and renal biopsy/autopsy reports are consistent with a clinical diagnosis of MCKD2 (Thompson et al., Arch. Intern. Med., 138, 1614-17 (1978)).

FIG. 2 depicts the integrated physical and genetic map of the FJHN/MCKD2 candidate region on chromosome 16p. Genetic STRP markers and their relative locations are indicated on the left. Locations of significant linkage results (LOD scores >3.0) are indicated for 2 families in the current report (Family 1 and Family 2) and for five other studies (referenced 1-5). Nine known STRPs and nine novel STRPs were identified, localized and genotyped. Two novel STRP loci were identified in BAC2349B8; the position of these loci (2349B8(16)-2 and 2349B8(16)-1) are separated by 54,000 bp as indicated in FIG. 2, and the order of these are given in FIG. 3. Genetic loci identified in the region are indicated to the right of the figure.

FIG. 3 depicts the haplotype results indicating the minimal genetic interval on chromosome 16 segregating with the FJHN phenotype in Family 1 and Family 2. FJHN affected individuals are indicated by shaded symbols, white circle and squares indicate unaffected family members, slash indicates deceased. Genetic STRP loci genotyped are listed in positional order in the left column for each family. Haplotypes segregating with the disease locus are shaded. Individual II-5 from Family 2 is unaffected, but has inherited the disease associated haplotype for the interval D16S412-D16S3046, indicating this region does not contain the FJHN disease locus. The boxed region indicates the minimal haplotype region segregating with the FJHN in both families, indicating the FJHN gene is within the interval flanked by 2349B8(16)-2 and D16S3046.

FIG. 4 depicts the structure of the human UMOD gene. A. Genomic organization of the UMOD gene. The exons and introns are represented as vertical boxes and horizontal lines respectively. The sizes of each intron are given in bp. B. cDNA structure of the UMOD gene. The translation start and stop codon are labeled as ATG and TGA, respectively. The 5′ and 3′ untranslated regions are shaded gray. The arrows indicate the missense mutations identified in this study. The horizontal bar indicates the deletion identified in this study. C. Structure of the wild-type UMOD protein. The inititation met is amino acid 1. The signal peptide is shown as a black box. The EGF-like domains are shown as dotted lines. The ZP domain is shown as a gray box. The eight potential glycosylation sites are shown as Y. The missense mutations identified in this study are shown as arrows with the corresponding amino acid listed below. The 9 amino acid deletion is shown as a horizontal bar. Additional recent preliminary data suggest that additional exons, other than those depicted in FIG. 4, may exist.

FIG. 5 diagrams mutations in the UMOD sequence. The top sequence in each panel shows wild-type sequence (SEQ ID NO:1 to SEQ ID NO:4). The bottom sequence is from an affected individual (SEQ ID NO:5 to SEQ ID NO:8). Descriptions of each mutation are given for [genomic; cDNA; protein] in accordance with nomenclature guidelines. A. Affected individuals in Family 1 were heterozygous for a 27 bp deletion that results in the in-frame deletion of amino acids 177-185. [g.1966_1992de1; c529_555del; p.H177_R185del]. B. Affected individuals in Family 2 were heterozygous for a missense mutation that changes a conserved cys to tyr. [g.1880G>A; c.443G>A; p.C148Y]. Affected individuals in Family 3 were heterozygous for a missense mutation that changes a gly to a cys. [g.1744G>T; c.307G>T; p.G103C]. D. Affected individuals in Family 4 were heterozygous for a missense mutation that changes a conserved cys to arg. [g.2086T>C; c.649T>C; p.C217R].

FIG. 6. Alignment of the amino acid sequence of human UMOD (GenBank accession No M17778 (SEQ ID NO:9)) with the UMOD of bovine (GenBank accession No 575958(SEQ ID NO:10)), murine (GenBank accession No NM_009470(SEQ ID NO:11)) and rat (GenBank accession No. M63510(SEQ ID NO:12)). All 48 C residues are conserved and shown in bold with an asterisk. The arrows indicate the position of the missense mutations identified in this study. The 9 amino acids deleted in Family 1 are indicated in bold and underlined.

FIG. 7 depicts SEQ ID NO:1 to SEQ ID NO:8 discussed herein.

FIG. 8 depicts SEQ ID NO:9 discussed herein.

FIG. 9 depicts SEQ ID NO:10 discussed herein.

FIG. 10 depicts SEQ ID NO:11 discussed herein.

FIG. 11 depicts SEQ ID NO:12 discussed herein.

FIG. 12 depicts SEQ ID NO:13 discussed herein.

FIG. 13 depicts SEQ ID NO:14 discussed herein.

FIG. 14 depicts SEQ ID NO:15 discussed herein.

FIG. 15 depicts SEQ ID NO:16 discussed herein.

FIG. 16 depicts SEQ ID NO:17 discussed herein.

FIG. 17 depicts SEQ ID NO:18 discussed herein.

FIG. 18 depicts SEQ ID NO:19 discussed herein.

FIG. 19 depicts SEQ ID NO:20 discussed herein.

FIG. 20 depicts SEQ ID NO:21 discussed herein.

FIG. 21 depicts SEQ ID NO:22 discussed herein.

FIG. 22 depicts SEQ ID NO:23 discussed herein.

FIG. 23 depicts SEQ ID NO:24 discussed herein.

FIG. 24 depicts SEQ ID NO:25 discussed herein.

FIG. 25 depicts SEQ ID NO:26 discussed herein.

FIG. 26 depicts SEQ ID NO:27 discussed herein.

FIG. 27 depicts SEQ ID NO:28 discussed herein.

FIG. 28 depicts SEQ ID NO:29 discussed herein.

FIG. 29 depicts SEQ ID NO:30 discussed herein.

FIG. 30 depicts SEQ ID NO:31 discussed herein.

FIG. 31 depicts SEQ ID NO:32 discussed herein.

FIG. 32 depicts SEQ ID NO:33 discussed herein.

FIG. 33 depicts SEQ ID NO:34 discussed herein.

FIG. 34 depicts SEQ ID NO:35 to SEQ ID NO:57 discussed herein.

FIG. 35 depicts SEQ ID NO:58 to SEQ ID NO:87 discussed herein.

DETAILED DESCRIPTION OF THE INVENTION

The invention provides a method of diagnosing a disease or a predisposition to contract a disease by assaying for mutations of UMOD within a test subject. Any individual can be tested in accordance with the inventive method. Typically, however, the test subject (or patient) belongs to a family with a history of disorders such as, for example, MCKD2, FJGN, nephropathy, renal failure, hyperuricemia, gouty arthritis, and enuresis. Asymptomatic individuals from such families can be tested to assess whether they have a predisposition to contract such diseases or whether they might be a carrier of an allele that can cause the disease in their progeny. In fact, the method can be used prenatally to assess the propensity of a fetus to develop MCKD2, FJGN, nephropathy, renal failure, hyperuricemia, gouty arthritis, and enuresis after birth. Alternatively, the inventive method can be used to diagnose symptomatic patients, typically those exhibiting hyperuricemia, renal insufficiency, and/or enuresis. For such patients, the inventive method can provide earlier and/or more definitive diagnosis, which can facilitate earlier intervention and treatment. Furthermore, inasmuch as people in need of transplants often receive donated kidneys and other renal tissue from close relatives of family members, the inventive method can be used to screen donors or donated tissue to ensure that the recipient does not receive renal tissue that produces abnormal UMOD protein.
In one embodiment, the inventive method involves assaying genetic material obtained from a test subject. The genetic material can be, for example, DNA or RNA obtained directly from the test subject, or the genetic material can be copied or amplified from genetic material within the test subject's cells (e.g., via PCR, RT-PCR, or other suitable technique). For example, cells can be harvested from a urine sample to obtain genetic material. To ensure that sufficient quantity of genetic material is available for testing, typically genetic material amplified from cells obtained from the test subject is assayed in accordance with the inventive method. Desirably, a PCR or RT-PCR strategy is employed using primers flanking all or a portion of the UMOD gene, so as to amplify this sequence from the patient for the assay. Because MCKD2 and/or FJGN are autosomal dominant disorders, it is most preferred to amplify/copy both copies of the UMOD gene from the test subject, so that both can be assayed in accordance with the inventive method.
However obtained, the genetic material is assayed to detect a mutation in the UMOD gene (e.g., a mutation at least one of the two UMOD alleles). Any test able to detect mutations appropriate to the type of genetic material (e.g., gDNA, cDNA, RNA, etc.) can be used to this end. For example, a portion or substantially all of the genetic material can be sequenced, and the sequence compared to the wild-type UMOD sequence (see, e.g., GenBank Accession Nos. AY 162963 (SEQ ID NO:13), AY162964(SEQ ID NO:14), AY162965(SEQ ID NO:15), AY162967(SEQ ID NO:16), AY162968(SEQ ID NO:17), AY162969(SEQ ID NO:18), and AY162970(SEQ ID NO:19)) to detect any mutations (see, e.g., FIG. 5). Alternatively, the genetic material can be probed with a hybridization probe that is substantially specific for a predetermined UMOD mutation (e.g., via Northern or Southern hybridization, PCR, or other appropriate method, such as are well-known to those of ordinary skill in the field). For example, one known UMOD mutation associated with MCKD2 and/or FJGN is a deletion of 27 base pairs from exon 4 of the UMOD gene (see FIG. 6), and a probe designed to straddle this deletion can be employed to quickly assay for this mutation (e.g., via ELISA).
In another embodiment, the inventive method involves assaying UMOD protein obtained from the test subject. The UMOD protein can be obtained by any suitable method, such as in a urine sample or cells isolated therefrom. Thereafter, the UMOD protein obtained from the test subject is assayed to detect a mutation. For example, the UMOD protein can be purified (either partially or substantially (see, e.g., Tamm and Horsfall, J. Exp. Med., 95, 71-97 (1952)) and assayed via immunohistological techniques (e.g., Western blotting, ELISA, immunoprecipitation, etc.) using one or more antibodies recognizing known mutant UMOD proteins but not wild type UMOD protein. Alternatively, or in conjunction, the UMOD protein sample from the test subject can be assayed using one or more antibodies recognizing wild type UMOD proteins but not known mutant UMOD protein. Thus, in some applications, it can be possible to develop an immunological UMOD profile of a given test subject or even quantitatively determine the amount and/or type of mutant and wild type UMOD protein present.
As an alternative to immunological characterization, protein from a test subject can be assayed morphologically. In this respect, UMOD is known to be polymeric in its native form, composed of monomeric subunits of approximately 85 kD, with 30% of the molecular weight due to carbohydrates and the remaining 70% due to the polypeptide chain (Fletcher et al., Biochem. J, 120, 425-32 (1970)). Electron microscopy reveals that the high molecular weight aggregate is composed of thin, intertwining fibers with a zigzag or helical structure. Recent analysis indicates that the filaments consist of two protofilaments wound around each other, forming a right-handed helix (Jovine et al., Nat. Cell. Biol., 4, 457-61 (2002)). UMOD contains a zona pelucida (ZP) domain, which has been shown to be responsible for polymerization of ZP-containing proteins into filaments (Jovine et al.). UMOD also contains a high number of cysteine residues (48 per monomer), allowing for the potential formation of 24 intramolecular disulfide bonds. These cysteine residues are highly conserved across species (FIG. 6). Mutations of the UMOD protein can alter its primary and secondary structure and ability to associate and form its typical tertiary structure. Thus, in some applications, it is possible to compare the structure of UMOD from a test subject with that of wild type protein as a morphological assay for mutant UMOD protein.
Of course, it also is possible to employ both genetic and protein assays in conjunction with each other to detect mutant UMOD within a test subject. Regardless of the method of assay, however, a test result that supports the presence of mutant or abnormal UMOD genetic material and/or protein from the test subject supports a diagnosis of MCKD2, FJGN, nephropathy, renal failure, hyperuricemia, gouty arthritis, or enuresis within the test subject, if accompanied by other symptoms consistent with such a disease. A UMOD-positive result for a non-symptomatic test subject supports a diagnosis of a predisposition to develop such a disease.
The following example further illustrates the invention but, of course, should not be construed as in any way limiting its scope.

EXAMPLE 1

This example demonstrates the existence of four UMOD gene mutations that segregate with the disease phenotype in three families with FJGN and in one family with MCKD2. These findings provide direct evidence that MCKD2 and FJGN arise from mutation of the UMOD gene and are allelic disorders. Accordingly, it is possible to assay for UMOD mutations to identify a propensity to develop FJHN and/or MCKD2.

Patients and Methods

Pedigrees and Diagnostics
Study participants were obtained from four families. Family 1 was a large multi-generational family in which the disorder was traced back 7 generations. The family tree contains more than 300 members and was too large for the entire pedigree to be depicted. FIG. 1 shows the pedigree for selected portions of the family in whom the majority of samples were obtained. This family had a long history of hyperuricemia, reduced fractional excretion of uric acid, and renal failure, inherited in an autosomal dominant fashion, with clinical findings consistent with FJHN. Family 2 was a large multi-generational family that also segregated FJHN as a highly penetrant autosomal dominant trait. Family 3 has previously been reported to suffer from medullary cystic disease, hyperuricemia, and gout (Thompson et al., Arch. Intern. Med., 138, 1614-17 (1978)), inherited in an autosomal dominant fashion (see FIG. 1). A sample was obtained from one affected family member from Family 4. Family 4 was previously extensively described in the literature as suffering from familial hyperuricemia and renal disease but no medullary cysts, findings consistent with a diagnosis of FJHN (Massari et al., Arch. Intern. Med., 140, 680-84 (1980)). Family 5 was screened because family members had exhibited symptoms consistent with a diagnosis of FJGN.
Serum uric acid and serum creatinine measurements were performed, and 24-hour urine collections for uric acid and creatinine were obtained. The creatinine measurements were performed by the Jaffe alkaline picrate kinetic method (Tietz N W. Clinical Guide to Laboratory Tests, 3d edition. WB Saunders Company, Philadelphia, Pa.; 186-87 (1995)). The uric acid measurements were performed on the ADVIA 1650 Chemistry System. The uric acid determination method is based on the Fossati enzymatic reaction using uricase with a Trinder-like endpoint (Fossati, Clin. Chem., 26, 227-231 (1980)). Estimates of creatinine clearance, as determined by the Cockroft-Gault formula (Cockroft et al., Nephron, 16, 31-41 (1976)), were made using the patient's weight or ideal body weight, whichever was less. Renal insufficiency was defined as an estimated creatinine clearance less than 80 ml/min. Enuresis was defined as persistent bed-wetting after the age of 4 years.
Patients were considered to be definitely affected if they met the following criteria: (1) Hyperuricemia, defined as serum uric acid levels greater than 2 standard deviations (s.d.) above the age- and gender-adjusted norms for the population (Wilcox, J. Pediatr., 128:731-41 (1996); Mikkelsen et al., Am. J. Med., 39, 242-51 (1965)) or a history of gout and current treatment with allopurinol, and (2) Reduced fractional excretion of uric acid (<5% for men and <6% for women) or a reduced creatinine clearance of less than 80 ml/min. (In general, individuals with a creatinine clearance less than 80 ml/min will start developing an elevated fractional excretion of uric acid (Rieselbach et al., Nephron, 14, 81-87 (1975)), and as such family members with renal insufficiency could not have their fractional excretion of uric acid used as a determinant of FJHN). Family members were defined as clinically unaffected if the serum uric acid level was within 1 s.d. of the age and gender-adjusted norms for the population (Wilcox; Mikkelsen et al.).
DNA-Marker Analysis
Genomic DNA was extracted from peripheral blood by standard methods using the QIAamp blood kit (Qiagen). Genetic linkage studies were performed for 90 individuals from two extended multigenerational families diagnosed with FJHN (Family 1 and Family 2, FIG. 1). Available family members were genotyped for STRP-type (Short Tandem Repeat Polymorphism) genetic markers spanning the candidate interval. In addition to 9 previously reported STRP loci, 9 novel STRP loci were developed from a 5.6-Mb physical map of the interval (FIG. 2, FIG. 3). These marker loci were PCR amplified by use of fluorescence-labeled primers, permitting genotyping by conventional methods (Hart et al., Am. J. Hum. Genet., 70, 943-54 (2002)). PCR products were detected by an ABI 377 fluorescent sequencer and were analyzed by GENESCAN 2.1 (Applied Biosystems).
Parametric Linkage Calculations: LOD Scores and Haplotype Analysis
Sub-localization of the candidate interval was achieved by means of genetic linkage studies and determination of the minimal region of overlap of haplotypes segregating with the FJHN trait in Family 1 and Family 2. Standard two-point and multipoint linkage analyses were performed using the VITESSE program (O′Connell et al., Nat. Genet., 11, 402-08 (1995)). Assumptions of the linkage analyses included autosomal dominant transmission, penetrance values of 95-100%, a disease allele frequency of 0.0001, and a phenocopy rate of 1%. To permit identification of haplotypes, a physical map of the FJHN candidate gene region was developed. This map permitted precise localization of known STRP markers within the region and allowed identification of novel STRP markers at desired locations spanning the interval.
Development of a Physical Map of the Candidate FJGN Candidate Interval; STRP and Gene Identification
To identify novel STRP-type markers spanning the candidate interval and to permit identification of all known and hypothetical genes within the interval, the development of a detailed physical/genetic map was initiated (Zhang et al., Cyto. Genet. Cell. Genet., 95, 146-52 (2001)). The final alignment contained 67 BACS that span a 5.6 million base region. This region contains two gaps across which a BAC sequence did not align. This contig was screened for all known genes, and STRP loci were identified through the NCBI Human Genome Sequencing website and GENEMAP 99 gene website [on the internet at www.ncbi.nlm.nih.gov/genome/seq and www.ncbi.nlm.nih.gov/genemap/] gene and STRP loci confirmed on the BAC contig were positioned on the new map. New STRP markers were identified using the Tandem Repeats Finder (Benson, Nucl. Acids. Res., 27, 573-80 (1999); and on the internet at c3.biomath.mssm.edu/trf.advanced.submit.html). Candidate STRP sites were then selected and primers designed using Oligo 4.0 software.
Several sources of information were used to identify genes in the candidate region: The Human Genome Project Working Draft at UCSC (on the internet at genome.ucsc.edu/), the Sanger Center's ENSEMBLE database (on the internet at www.ensembl.org) and Locus Link (Benson). NCBI BLAST (on the internet at www.ncbi.nlm.nih.gov/blast/) and ePCR were also used on the BAC contig sequence with the BLAST non-redundant and dbEST databases screened. A cDNA contig was made for each candidate gene using all information that was available at the time. The inclusion of all EST data provided for a more accurate representation of the gene. Intron/exon boundaries were determined manually using the consensus splice sequences indicated at GENIO/splice (internet site is genio.informatik.uni-stuttgart.de/GENIO/splice/). Primers for amplifying candidate genes from genomic DNA were designed using data obtained from the primary contig as well as from available NCBI data (accession numbers in electronic references; NCB Locus Link, NCBI Entrez) [NCBI Locus Link (on the internet at www.ncbi.nlm.nih.gov/LocusLinc/) for genes shown in FIG. 2—Locus ID Numbers are: XT1-64131 (SEQ ID NO:20), COQ7-10229 (SEQ ID NO:21), B/K-51760 (SEQ ID NO:22), G104-162074, GPRC5B-51704 (SEQ ID NO:23), GP2-2813 (SEQ ID NO:24), UMOD-7369 (SEQ ID NO:25), BUCS1-116285 (SEQ ID NO:26); NCBI Entrez provided at (www.ncbi.nlm.nih.gov/Entrez/) Gene Accession Numbers: XT1-XM 485032 (SEQ ID NO:27), COQ7-NM 016138 (SEQ ID NO:28), B/K-NM 016524 (SEQ ID NO:29), G104-XM_091332 (SEQ ID NO:30), GPRCSB-NM_016235 (SEQ ID NO:31), GP2-NM_001502 (SEQ ID NO:32), UMOD-NM_003361 (SEQ ID NO:33), BUCS1-NM_052956 (SEQ ID NO:34)]. By means of linkage and haplotype analyses, the FJHN candidate region was refined to about an 1.7-Mb interval. Five known genes were localized to this interval. Additionally, using an integrated bioinformatic and bench lab approach, one previously uncharacterized genetic locus was localized within the interval. All exons and intron-exon boundaries of four of these genes were analyzed by sequence analysis of genomic DNA from affected and unaffected family members from Family 1 and Family 2.
UMOD Exon Sequencing
The genomic structure of the UMOD gene was determined bioinformatically and was confirmed by sequence analysis. Oligonucleotide primers to amplify 11 of the 12 exons, including intron-exon boundaries (Table 1), were designed with Oligo 4.02 (National Biosciences). PCR amplification of the UMOD gene was performed as indicated in Table 1.

TABLE 1

Primer Sets for Exonic
Amplification of Human UMOD Gene

Primer (5′→3′)

	SEQ		SEQ				GenBank
	ID		ID		Size	PCR	Accession
Exon	NO	Forward	NO	Reverse	(bp)	Condition^a	Number

02-03	35	TCCTGCTCCAAATGACTGAGTTCT	36	TCAACCCAATGGAATGACCTCTTA	888	B	AY162963

04-05	37	GGTGGAGGCTTGACATCATCAGAG	38	GGAATAGGGCTCAGATGGTCTTTG	1493	A	AY162963

04-05^S	39	GCCCTGGCCTCATGTGTCAATGTG	40	GGGTCACAGGGACAGACAGACAAT			AY162963

04-05^S	41	CGGCGGCTACTACGTCTACAACCT	42	GTAGCTGCCCACCACATTGACACA			AY162963

06	43	ACCTCTGGACCTCAAGTAATCTGT	44	TGATGCCTACTGGCTGAGACAATC	940	A	AY162964

07	45	ACCAGCAGATTTAGCTTTGAAGTC	46	GCTTGAACCAGGCAGTGCTTTGAC	475	A	AY162965

08	47	AGCAGCATCCAGGCACTTGTCAGA	48	TGAGGCAGAAGAATCACTTGAACC	711	B	AY162967

08^S			49	TCCAAAGACCCCCTCTGAATTCTA			AY162967

09	50	ATTTGAATCCAGGAAGTCTGACTC	51	GGCAAGCCACTGAAGTTCTCTGAG	612	B	AY162968

10	52	GAGCGGCTCAGAGAACTTCAGTGG	53	CCCGTGTCCTGTGTTACATTCATC	529	B	AY162968

11	54	GAGCCCCTGATGGGTCTGAAGTAG	55	TCTGAGCCACTCTCCTTATTTAGA	345	B	AY162969

12	56	TAGATTGGGCACTTCACAAGAATG	57	ACAGCAGAACCCAGTCTCACTGAG	733	B	AY162970

^Sdenotes primers also used in sequencing reactions. Sequencing was performed with BigDye Terminator System form ABI.
^aThe standard PCR amplification for each exon contains: taq (0.025 U/μl), 1x PCRx Enhancer Buffer, 25 nM each dNTP, and 1.5 mM MgS04 A = 5% PCRx Ehancer
B = 1X PCRx Enhancer Buffer, no PCR x Enhancer.
Cycling Conditions = 95-5′+94-30″/56-30″/72-90″ 35X+71-10′

Amplified DNA was purified with the QIAquick PCR Purification Kit (Qiagen) and was sequenced using the BigDye Terminator Cycle Sequencing Kit on an ABI 3700 DNA Analyzer (Applied Biosystems) by the Genomics and Proteomics Core Laboratories of the University of Pittsburgh. Sequence analysis was performed with Sequencher 4.1 software (GeneCodes).

Results

Clinical Findings
Over a five-year period, clinical testing was performed on 72 members of Family 1. Thirty-one met strict criteria to be considered affected (hyperuricemia with reduced fractional excretion of uric acid or renal insufficiency), 22 were diagnosed as normal, and there were 10 unaffected spouses. For nine family members, a certain diagnosis could not be made. Thirty-four individuals suffered from hyperuricemia and 28 suffered from renal insufficiency. The pedigrees for families 2 and 3 identify all individuals who suffered from hyperuricemia or renal insufficiency.
Renal Biopsies
Pathologic samples were obtained by kidney biopsy in three members of Family 1. All three biopsies revealed histological changes of tubular atrophy and interstitial fibrosis. Global glomerulosclerosis was present, and there was no evidence of glomerulonephritis. In Family 2, a biopsy specimen of an affected female at age 39 years revealed widespread tubular atrophy. In Family 3, several autopsy specimens were obtained. The first was that of a 34-year-old man, revealing by report, tubules ensheathed by a dense acellular hyaline material (Thompson et al., Arch Intern Med., 138, 1614-17 (1978)). Medullary cysts were present. In another family member, autopsy studies again revealed sheathing of the tubules by fibrous tissue. In case three, tubules were ensheathed by dense acellular hyaline material (Thompson et al.). In Family 4, biopsy samples revealed focal tubular atrophy with interstitial fibrosis and lymphocytic infiltration. In summary, all biopsy specimens revealed focal tubular atrophy with interstitial fibrosis. Autopsy reports revealed tubules ensheathed by dense acellular hyaline material. Interstitial deposits of PAS-positive material also have been identified in medullary cystic kidney disease (Zager et al., Lab. Invest., 38, 52-57 (1978); Resnick et al., Lab. Invest., 38, 550-55 (1978)). Immunostaining of these deposits was found to be markedly positive with antibody to Tamm-Horsfall protein.
Physical Map of the Candidate Interval
Existing genetic and physical maps of the FJHN/MCKD2 candidate interval were generally poorly integrated and identified relatively few polymorphic genetic markers (STRPs) spanning the interval. This was problematic as a key marker (D16S3056) was uninformative in the families studied. The development of an integrated physical and genetic map of the FJHN/MCKD2 candidate interval (summarized in FIG. 2) permitted precise orientation of the results of previous linkage studies, to precisely localize known genes to the candidate interval, and to develop novel STRP loci. The availability of novel STRP markers permitted refinement of the candidate interval by haplotype analysis. The location of eight known and eight novel STRPs are shown in FIG. 2. Oligonucleotide primers and conditions used to amplify these STRPs are shown in Table 2.

TABLE 2

Primer Sets used in the
amplification of STRP loci.

Primer (5′→3′)

	SEQ		SEQ		STRP^a
	ID		ID		Size	STRP	Relative
Locus	NO	Forward	NO	Reverse	(bp)	Type	Position^b

D16S499	58	TCTCACAGTTCTGGAGGCTGGAAG	59	GGTGGACCCTAATTGCATAGGATTG	210	CA Repeat	238,700

D16S501	60	TGTCCTCTAGGGGAAGAGATGTCT	61	AGGTCAGGGACCTAGTAACTACTC	260	CA Repeat	305,100

481E9(16)	62	CCAGAGCCCTACAGGAGTGTACTG	63	CAAGACCAGGGGATCACAGTAACT	320	Di	362,700

449G13(16)	64	CAGCCTGGGCAACAGAGACTC	65	AGGCGCTAAATTCAGAGCAAATAG	300	CA Repeat	1,784,000

419L9(16)	66	GCTGTAATGGTGCTGTGTAAATCT	67	AAGAATCCTCCAGACTTCATACAC	218	CA Repeat	1,983,000

626G11(16)	68	ATCAGCTTAGCAGACATCTCTTCC	69	CTTGTAGTCCCAGCTACTCAGTGG	292	CA Repeat	2,019,000

234B8(16)-2	70	CACGAGAATCCCTTGAACCTG	71	TGGCTCTCCACTCAGAGATTC	214	Penta	2,050,000

2349B8(16)-1	72	CTGTGGCTGGCTTGTTTCACTCAG	73	TTGGGTGGAGGCAATCCAAGTGTC	201	CA Repeat	2,133,000

363E6(16)	74	TGTGTTATTGGTGAAATGCACATA	75	GGTGGCTCATGCCTGTAATTTGAG	355	Di	2,250,000

D16S3041	APPLIED BIOSYSTEM LINKAGE MAPPING SET, PANEL 73	270	CA Repeat	2,310,000

D16S490	76	TGACAGGCACATAGATTATTATGC	77	CGTACCCGGCTGATTATTTTAGAT	357	Tetra	2,390,000

D16S3036	78	AGATAGGGGTCTAGTTTCATTATC	79	ACAAAGCTGGACATATCACACTAC	310	CA Repeat	2,450,000

2380F24(16)	80	AGGCTGGTCTCGAACTCCTGACCT	81	GGGACTACAGGTGTGTGAATTTGA	272	Di	2,730,000

D16S3046	APPLIED BIOSYSTEM LINKAGE MAPPING SET, PANEL 22	110	CA Repeat	3,650,000

D16S3045	82	AGGACGGCTGAATGTCTGTCATCA	83	TTGGGGAGTCCCTAAATGACTTTA	180	CA Repeat	3,790,000

14O15(16)	84	GGCAGAAATGGCACATCTTAACTA	85	CAGCCTGGGTGACAGAGTGAGACT	234	CA Repeat	5,040,000

D16S403	APPLIED BIOSYSTEM LINKAGE MAPPING SET, PANEL 73	150	CA Repeat	5,820,000

D16S412	86	ACCCAGTAGAGACCCATCTTACTC	87	ACCCAGTAGAGACCCATCTTACTC	180	CA Repeat	5,952,000^c

^aSTRP size indicates the region that the PCR amplified band will be in.
^bRelative position refers to the locus location on the BAC contig alignment sequence
^cThis position determined using the Human Genome Project data from June 2002
Amplifications performed using standard Amplitag Gold Conditions

The consensus candidate interval for most reports, including the present linkage data, support a candidate interval located in 16p13.11 (D16S499) to 16p12.2 (D16S403). It is apparent from FIG. 2 that, while all linkage intervals reported for FJHN and MCKD2 map to chromosome 16p, not all overlap.
Linkage Analyses
Results of genetic linkage analyses localized the gene for FJHN in two of the families (Family 1 and Family 2) to an overlapping interval of about 1.7-Mb (FIG. 2). For Family 1 the gene was localized to an interval of about 3.8-Mb delineated by 2349B8(16) to D16S403 (Z_MAX=12.5 @ D16S3041, θ=0.01) and for Family 2 the linkage interval was ˜17-Mb between D16S404 and D16S3046 (Z_MAX=3.2 @ D16S3041, θ=0.00); D16S404 extends about 14-Mb telomeric to D16S499. These findings were consistent with four (Dahan et al., J. Am. Soc Nephrol., 12, 2348-57 (2001); Hateboer et al., Kidney Int, 60, 1233-39 (2001); Scolari et al., Am. J. Hum. Genet., 64, 1655-60 (1999); Stiburkova et al., Am. J. Hum. Gen., 66, 1989-94 (2000)) of the previous 5 reports of linkage for FJHN to chromosome 16p. The present candidate interval did not overlap that of the fifth study (Kamatani et al., Arthritis Rheum., 43, 925-29 (2000)) possibly reflecting genetic heterogeneity (they are the only group to study Japanese FJHN families).
Candidate Gene Evaluation; Mutation Analyses
Integration of all known linkage reports for FJHN with the present linkage data identified an interval of minimal overlap (<0.3-Mb) from 2349B8(16) to D16S3036 for the present linkage results with those of Dahan and co-workers (see FIG. 2) [Dahan et al., supra]. This gene identification approach identified 1 known gene (B/K protein; NM_016524) and one hypothetical gene (G104; XM_091332) in this common interval. Direct sequence analysis of genomic DNA from affected and unaffected family members from Family 1 and Family 2 for coding regions (including intron-exon junctions) of the B/K gene and the hypothetical gene G104 did not identify any alterations of DNA that would account for the FJHN trait in either family.
Because the definitive diagnosis of FJHN can be problematic (particularly in milder cases and in younger individuals), and incorrect diagnosis of family members can directly affect the boundaries of the candidate gene region, the present analysis proceeded using only linkage and genotype data from Family 1 and Family 2. Thus individuals who could not be diagnosed as affected based on the diagnostic criteria stated above were excluded from the present analysis. Similarly, individuals who did not have both normal renal function (calculated creatinine clearance greater than 100 ml/min) and a serum uric acid level within 1 s.d. of the mean adjusted for age and gender (Wilcox; Mikkelsen et al.) were excluded from the analysis to refine the candidate interval.
Haplotype analysis permitted the identification of the smallest common haplotype segregating with the FJHN trait in Family 1 and in Family 2 (FIG. 3). The present sequence analysis had excluded the known (B/K protein) and hypothetical gene (G104) from the interval 2349B8(16)-D16S3036, to permit refinement of the candidate interval to about 1.2-Mb, from D16S3036-D16S3046. This revised candidate interval contains 4 genes: butyrl coenzyme A synthetase 1 (BUCS1); glycoprotein 2 (GP2); G protein coupled receptor, family C group 5, member B (GPRCSB); and UMOD. Sequence analyses of GPRCSB and UMOD were performed for genomic DNA from affected and unaffected family members. No coding region polymorphisms were detected in the GPRCSB sequence data. To determine the genomic organization of the entire UMOD gene, all available UMOD mRNA and EST data were aligned to identify any possible splice variants. Using bioinformatic approaches, the genomic structure of the UMOD gene was determined (see FIG. 4). This approach led to the identification of 12 UMOD exons, which is one exon more than previously reported (Pennica et al., Science, 236, 83-88 (1987)). The novel exon identified by the present approach and supported by EST data is exon 2. Exons 1 and 2 are non-coding with the ATG start site in exon 3. Based upon EST data, there appear to be alternate 5′ transcription start sites so that transcription either begins with exon 1 and proceeds to exon 3 or transcription begins in exon 2 and proceeds to exon 3. In either case, the resultant protein is identical.
UMOD sequence analysis was undertaken on Families 1 and 2. Results of sequence analysis revealed 2 different mutations in exon 4 of UMOD in Families 1 and 2 (FIG. 5A, 5B). Mutations are described according to nomenclature guidelines (Antonarakis, Hum. Mutat., 11, 1-3 (1998); Den Dunnen et al., Hum. Mutat., 15, 7-12 (2000)). In each family, (g.1966_1992del in Family 1 and g.1880G>A in Family 2), the UMOD exon 4 gene mutation segregated completely with the disease phenotype. To evaluate the possible involvement of UMOD mutations in MCKD2, sequence analysis on 3 affected and 5 unaffected family members from a smaller family segregating MCKD2 (Family 3, FIG. 1) was conducted. Analysis of this family identified a third novel mutation (g.1744G>T) in UMOD, also in exon 4 (FIG. 5C). To evaluate the generality of UMOD mutations in FJHN, we performed mutational analyses on an affected member from an extended kindred previously reported (Massari et al., Arch. Intern. Med., 140, 680-84 (1980)). This analysis revealed a fourth novel mutation (g.2086T>C) in exon 4 of UMOD (FIG. 5D). Affected individuals in family 5 contained another mutation (g.2105G>A, c.668G>A, p.C223Y).
The specific UMOD gene mutations in Family 1, Family 2 and Family 3 each segregated in affected family members (FJHN in Family 1 and Family 2; and MCDK2 in Family 3). None of these mutations were identified in any of the 100 control chromosomes tested. Sequence analysis of the UMOD gene in 50 Caucasian controls (100 chromosomes) did reveal the presence of two silent polymorphisms within UMOD Exon 4. A previously reported synonymous SNP (Pirulli et al., J. Nephrol., 14, 392-96 (2001)) located at C174, has a T allele frequency of 82% and a C allele frequency of 18% for our samples. A novel synonymous SNP located at V287, has a G allele frequency of 87% and an A allele frequency of 13%. No polymorphisms affecting the translation of UMOD were detected in any of the 100 control chromosomes examined.
Genotype-Phenotype Correlation
For Family 1, 36 family members carried the mutation and 26 family members did not. Thirty-two of 36 (89%) genetically affected individuals suffered from hyperuricemia (as defined in Methods, supra). Twenty-eight of 32 (88%) genetically affected family members had an estimated creatinine clearance less than 90 ml/min when measured after the age of 18 years. Ten of 36 (28%) individuals carrying the UMOD mutation suffered from enuresis. The fractional excretion of uric acid was less than 6% in all genetically affected men and less than 5% in all genetically affected women with an estimated creatinine clearance greater than 70 ml/min. (The fractional excretion of uric acid increases in patients as renal function declines (Rieselbach et al., Nephron, 14, 81-87 (1975))). Thirty-two of 36 individuals carrying the UMOD mutation met the strict clinical criteria required to be diagnosed as affected. The remaining four individuals were women who had normal serum uric acid levels despite low fractional excretions of uric acid. Two of these women had mild renal insufficiency. The serum uric acid levels remained normal or borderline on testing over several years in three of these women. Five family members who did not carry the UMOD mutation had serum uric acid levels which were elevated but which were not greater than 2 standard deviations above the mean.
In family 2, nine of nine patients with the mutation suffered from hyperuricemia, and 9 of 9 patients suffered from renal insufficiency. In Family 3, 2 of 3 family members carrying the mutation suffered from hyperuricemia, and all three affected family members suffered from renal insufficiency.
These data are surprising given that recently one study has excluded UMOD as a candidate gene for a large Italian family segregating MCKD2 (Pirulli et al., supra). Although this study reports that the entire UMOD coding region was sequenced, this was performed with different primer sets than those used in the current study. Methodological differences in sequencing of exon 4 might account for the different results, however, other possibilities must be considered. Deletion of an entire exon could result in PCR amplification of only the wild type allele, masking the presence of a mutation. Pirulli et al. did not analyze the non-coding exons 1 and 2, nor the 5′ regulatory region of UMOD. It is possible that mutations in exon 1, exon 2 or the regulatory region could result in loss of UMOD production (Salowsky et al., Gene, 293, 9-19 (2002); Flagiello, Mutations in brief no. 195. Online. Hum. Mutat., 12, 361 (1998)). Alternately, genetic heterogeneity may exist with another kidney specific gene located in the candidate interval.
All references, including publications, patent applications, and patents, cited herein are hereby incorporated by reference to the same extent as if each reference were individually and specifically indicated to be incorporated by reference and were set forth in its entirety herein.
The use of the terms “a” and “an” and “the” and similar referents in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. The terms “comprising,” “having,” “including,” and “containing” are to be construed as open-ended terms (i.e., meaning “including, but not limited to,”) unless otherwise noted. Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein, is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the invention.
Preferred embodiments of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Variations of those preferred embodiments may become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventors expect skilled artisans to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than as specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.

Claims

1.-20. (canceled)

21. An oligonucleotide comprising a fragment of a uromodulin (UMOD) gene or the complement thereof, wherein the UMOD gene comprises a imitation selected from the group consisting of:

(i) G>A at nucleotide position 1880 of the UMOD coding sequence;

(ii) a deletion of the nucleotides at positions 1966 to 1992 of the UMOD coding sequence;

(iii) T>C at nucleotide position 2086 of the UMOD coding sequence;

(iv) G>A at nucleotide position 2105 of the UMOD coding sequence; and

(v) G>T at nucleotide position 1744 of the UMOD coding sequence;

wherein the oligonucleotide is detectably labeled.

22. The oligonucleotide of claim 21, wherein the oligonucleotide specifically binds to the UMOD gene comprising a mutation under high stringency conditions.

23. The oligonucleotide of claim 21, wherein the oligonucleotide does not specifically bind to the wild type UMOD coding sequence under high stringency conditions.

24. The oligonucleotide of claim 21, wherein the UMOD gene comprises a deletion of the nucleotides at positions 1966 to 1992 of the UMOD coding sequence.

25. The oligonucleotide of claim 21, wherein the UMOD gene comprises a G>A mutation at position 1880 of the UMOD coding sequence.

26. The oligonucleotide of claim 21, wherein the UMOD gene comprises a T>C at nucleotide position 2086 of the UMOD coding sequence.

27. The oligonucleotide of claim 21, wherein the UMOD gene comprises G>A at nucleotide position 2105 of the UMOD coding sequence.

28. The oligonucleotide of claim 21, wherein the UMOD gene comprises G>T at nucleotide position 1744 of the UMOD coding sequence.

29. A method of detecting a mutation in a UMOD gene, the method comprising:

(a) contacting a UMOD nucleic acid obtained from a human test subject with an oligonucleotide selected from:

(i) an oligonucleotide comprising a fragment of a UMOD nucleic acid sequence that specifically binds to a UMOD gene having a mutation selected from the group consisting of:

(1) T>C at nucleotide position 2086 of the UMOD coding sequence;

(2) G>A at nucleotide position 2105 of the UMOD coding sequence; and

(3) G>T at nucleotide position 1744 of the UMOD coding sequence;

(ii) an oligonucleotide that is the complement of the oligonucleotide of (i);

(b) detecting hybridization of the oligonucleotide with the UMOD nucleic acid, wherein hybridization is indicative of the presence of a mutation in the UMOD gene.

30. The method of claim 29, wherein the UMOD nucleic acid is genomic DNA.

31. The method of claim 29, wherein the UMOD nucleic acid is RNA.

32. The method of claim 29, wherein the method further comprises generating a synthetic copy of the DNA or RNA of the test subject.

33. The method of claim 29, wherein the oligonucleotide is detectably labeled.