Mutations in a novel CLN6-encoded transmembrane protein cause variant neuronal ceroid lipofuscinosis in man and mouse

Abstract

The CLN6 gene that causes variant late-infantile neuronal ceroid lipofuscinosis (vLINCL), a recessively inherited neurodegenerative disease that features blindness, seizures, and cognitive decline, maps to 15q21-23. We have used multiallele markers spanning this approximately 4-Mb candidate interval to reveal a core haplotype, shared in Costa Rican families with vLINCL but not in a Venezuelan kindred, that highlighted a region likely to contain the CLN6 defect. Systematic comparison of genes from the minimal region uncovered a novel candidate, FLJ20561, that exhibited DNA sequence changes specific to the different disease chromosomes: a G-->T transversion in exon 3, introducing a stop codon on the Costa Rican haplotype, and a codon deletion in exon 5, eliminating a conserved tyrosine residue on the Venezuelan chromosome. Furthermore, sequencing of the murine homologue in the nclf mouse, which manifests recessive NCL-like disease, disclosed a third lesion-an extra base pair in exon 4, producing a frameshift truncation on the nclf chromosome. Thus, the novel approximately 36-kD CLN6-gene product augments an intriguing set of unrelated membrane-spanning proteins, whose deficiency causes NCL in mouse and man.

Figures

Figure 1

Narrowing the CLN6 region on human chromosome 15. A, Schematic of locations of DNA markers that delimit the genomic 15q22-23 DNA that must contain the CLN6 gene (top), drawn on the basis of data from the Human Genome Project (UCSC Human Genome Project Working Draft). Reported recombination events in families with vLINCL place the gene between D15S1020 and D15S216 (gray-stippled sections). The shared core Costa Rican haplotype points to the segment between MADH3gt and poly YE (black-stippled section). The middle line depicts genomic 15q23 DNA sequence, with the location of gaps (paired slashes), ESTs, and predicted and known genes (arrows) (UCSC Human Genome Project Working Draft). The location of FLJ20561 (blue) is shown, and its predicted exon-intron structure is given, with the coding region shaded (bottom). B, Results of haplotype analysis in Costa Rican and Venezuelan families. Alleles for DNA markers that span the CLN6 region are shown for 27 independent Costa Rican (CR1–CR27) and 2 Venezuelan (VZ1 and VZ2) disease chromosomes. Three chromosomes, distinguished by apparent recombination events (indicated by asterisks [*]), are from two affected Costa Rican siblings. Shared alleles (gray-shaded boxes) indicate a common haplotype that, for chromosomes CR1–CR15 also includes D15S1020, D15S1025, D15S1000, and D15S216 (not shown). Lack of allele sharing (unshaded boxes) at MADHG3gt and poly YE delimits a core Costa Rican haplotype and reveals an unrelated Venezuelan vLINCL chromosome. The “21”' allele at ITGA11ca is likely to be derived from the “19” allele by slippage. The MAP2K5ca “4”' allele is also common to normal chromosomes (see the “Material and Methods” section).

Figure 2

Candidate CLN6 mutations in human and mouse FLJ20561. A, G317T mutation, in exon 3, found on Costa Rican disease chromosomes. On the left are ABI Prism 377 sequence traces showing the reverse strand of exon 3 PCR products amplified from a normal control, from a Costa Rican patient (homozygote), and from a transmitting parent (heterozygote). The C→A change (underlined) results in the loss of an XhoI site, permitting a direct genotyping assay, the results of which are shown on the right. The ethidium bromide–stained agarose gel reveals two XhoI fragments (of 175 bp and 53 bp) for the normal allele and a single XhoI fragment (228 bp) for the mutant allele. The results demonstrate coinheritance of the mutant allele and clinically diagnosed disease (black square), inherited with the disease chromosome transmitted from each carrier parent (symbols containing dots), which is also detected in an unaffected carrier sibling. B, CTA deletion in exon 5 (producing the ΔY171 change in the protein), which is found on both Venezuelan vLINCL chromosomes. On the left are ABI Prism 377 sequence traces of the exon 5 products amplified from a normal control, from the affected Venezuelan child who is homozygous for the ΔY171 change, and from a heterozygous transmitting parent. The deletion produces a shorter (226 bp) PCR product, permitting a direct genotyping assay, the results of which are shown on the right. The autoradiograph shows radiolabeled exon 5 PCR products—226 bp for the mutant allele and 229 bp for the normal allele—found in the parents. C, Extra C-nucleotide insertion in exon 4 (producing the R103 frameshift change in the protein), which is found on the nclf chromosome. Shown are ABI Prism 377 sequence traces (for the reverse strand) of exon 4 PCR products amplified from wild-type mouse DNA and from nclf/nclf mouse DNA. Direct sequencing did not reveal this change in products amplified from several inbred strains of mice, from outbred mice, or from wild mice.

Figure 3

Human and mouse proteins encoded by FLJ20561 cDNA homologues. The top line in each pair shows the predicted 311-amino-acid open reading frame of the FLJ20561 cDNA. Below this line are differences unique to the 308-amino-acid mouse protein, predicted on the basis of the murine cDNA sequence. Sequences were aligned by BLAST 2 Sequences (also see the NCBI BLAST web site). Dashes (–) represent gaps in the match. The positions of six predicted introns (numbered 1–6), delineating seven exons, were determined by alignment of cDNA and genomic-DNA sequences (UCSC Human Genome Project Working Draft and Celera database). The stop mutation found on Costa Rican–haplotype disease chromosomes is indicated by an “at” symbol (@), the ΔY171 deletion mutation on Venezuelan disease chromosomes is indicated by an arrow, and the position of the frameshift, produced by the extra C nucleotide, on the nclf chromosome is indicated by an asterisk (*). The latter change leads to a stop codon after a run of 61 novel amino acids (PNAAAVYSLCQHHHFHHGSQHPPGGRLSQPSPALQWVPAPPVRQ REPHYQEPQAGDSDRLL&) that are not shown.

Figure 4

Comparison of human and mouse CLN6-gene products. A, Results of human and mouse multiple-tissue northern blots (Clontech), demonstrating wide expression, in brain and peripheral tissues. The human-adult-tissue northern blot was probed with an ∼700-bp FLJ20561 exon 7 probe, revealing an ∼2.4-kb mRNA, matching the size of the full-length cDNA. The mouse-adult tissue and whole-embryo northern blots were hybridized with a ∼1.1-kb probe (exons 2–7), which detects the 2.4-kb mRNA and an unexpected ∼5.5-kb band. A full-length FLJ20561 probe also detects a 5.5-kb band in human tissues (data not shown). P = pancreas; K = kidney; skM = skeletal muscle; Lv = liver; Lg = lung; Pl = placenta; B = brain; H = heart; T = testis; Sp = spleen; E17 = embryonic day 17; E15 = embryonic day 15; E11 = embryonic day 11; E7 = embryonic day 7. B, Hydropathy-plot overlay of predicted human and mouse proteins. Hydropathy plots, drawn according to the Kyte-Doolittle x-1 method (window length 19), by use of the Weizmann Institute of Science Genome and Bioinformatics, Protein Hydrophilicity/Hydrophobicity Search and Comparison server, are nearly identical for the human and mouse proteins, with the exception of the amino terminus. Positive values indicate calculated hydrophobic values. Conserved serine/threonine phosphorylation sites are indicated by circles. The location of the “Costa Rican” exon 3 stop codon is indicated by an “at” symbol (@); the “nclf” mouse exon 4 frameshift lesion is indicated by an asterisk (*), and the “Venezuelan” exon 5 ΔY171 change is indicated by an arrow. Below the plot is an alignment of the amino-terminal regions of the human and mouse proteins. A conserved putative N-myristoylation site (“lollipop” symbol) predicted by PredictProtein may become exposed on cleavage (vertical bar) of a putative presequence predicted by the PSORT II and CBS TargetP programs.