Analysis of two duplications of the LDL receptor gene affecting intracellular transport, catabolism, and surface binding of the LDL receptor

Two novel mutations of the low density lipoprotein (LDL)-receptor gene were found in two Italian familial hypercholesterolemia (FH)-heterozygotes. The first mutation was an 18 nucleotide duplication in exon 8 which is preceded by an A-->T transversion. The translation product of the mutant allele was predicted to be a receptor with an in-frame insertion of 6 amino acids in repeat B of the epidermal growth factor precursor homology domain. Analysis of LDL-receptor activity in the proband's fibroblasts showed a 50% reduction of 125I-labeled LDL binding and pulse-chase studies suggested that little, if any, of the mutant protein was processed to the mature form. The second mutation was a 7 kb duplication (from intron 2 to intron 6) of exons 3 through 6, predicted to encode an elongated receptor with the duplication of repeats 2-7 of the ligand binding domain. The elongated receptor was processed slightly more slowly than the normal receptor, but was converted to a mature form of the expected size. This mature, mutant receptor was degraded more rapidly than the normal receptor. On ligand blotting the elongated receptor bound twice as much LDL or beta-very low density lipoprotein (betaVLDL) as the normal receptor. In contrast, maximum binding of LDL to proband's cells was decreased to approximately 70% of the normal cells with a significant increase in apparent affinity. Cell association at 37 degrees C, internalization, and degradation showed a similar reduced maximum. Thus these mutations demonstrate that duplications of amino acid sequences in the low density lipoprotein LDL-receptor may disrupt the LDL-receptor pathway at different levels.

Cerebrotendinous xanthomatosis caused by two new mutations of the sterol-27-hydroxylase gene that disrupt mRNA splicing

Cerebrotendinous xanthomatosis (CTX) is an inherited sterol storage disease associated with the accumulation of cholestanol and cholesterol in various tissues. CTX is caused by a deficiency of sterol-27-hydroxylase, a mitochondrial enzyme that oxidizes the side chain of cholesterol in the pathway leading to the formation of bile acids. In the present study we report two mutations of sterol-27-hydroxylase gene (CYP27 gene) found in Italian CTX patients. Proband T.C. is homozygous for a G-->A transition at the first nucleotide of intron 7. This mutation causes the formation of minute amounts of an abnormal mRNA, in which exon 6 joins directly to exon 8 with the skipping of exon 7. The exon 6-exon 8 junction results in a frame shift, downstream from the codon for Arg362, which generates a string of 28 novel amino acids preceding a premature termination codon. Proband C.U. is homozygous for a G-->C transversion at the last nucleotide of exon 3. This mutation, which changes the consensus sequence of the 5' donor splice site, is associated with barely detectable levels of sterol-27-hydroxylase mRNA, of normal size, in proband fibroblasts. As both mutations change the sites for two restriction enzymes, rapid methods were devised for the identification of the healthy carriers among the probands' family members and for the screening of these mutations in other CTX patients.

Partial deletion of the gene encoding sterol 27-hydroxylase in a subject with cerebrotendinous xanthomatosis

An Italian subject with cerebrotendinous xanthomatosis (CTX) was found to have a partial deletion of the gene encoding the enzyme sterol 27-hydroxylase (CYP27 gene). Southern blot analysis revealed that this deletion (approximately 2 kb) spans from intron 6 to the 3' flanking (3'FLK) region, eliminating exons 7-9, the last three exons of CYP27 gene. No sterol 27-hydroxylase mRNA was detected in proband cells, either by Northern blot analysis or by reverse transcription polymerase chain reaction (PCR). This suggests that the mutant mRNA devoid of the exon encoding the whole untranslated sequence (exon 9) might be rapidly degraded in the cytoplasm. We used inverse PCR to obtain a partial sequence of the 3'FLK region of the normal CYP27 gene; this allowed us to define the mechanism underlying the deletion. The established sequence was used to design suitable primers to perform step-wise sequences of a 1.7 kb segment of the 3'FLK region of the normal gene and of the deletion joint in the CTX patient. The analysis of the sequence data indicate that the deletion might result from a complex mechanism involving two intragenic recombinations between a) two 14 nucleotide complementary sequences, one in intron 6 and the other in the 3'FLK region: and b) AT-rich complementary sequences of the 3'FLK region, and a slipped mispairing between two 6 nucleotide direct repeats, one in intron 6 and the other in the 3'FLK region. Such repeats are brought close to each other by the formation of the stem-loops induced by the two intragenic recombinations. This is the first example of CTX caused by a rearrangement of CYP27 gene.

Two novel partial deletions of LDL-receptor gene in Italian patients with familial hypercholesterolemia (FH Siracusa and FH Reggio Emilia)

In the present study we report two novel partial deletions of the LDL-R gene. The first (FH Siracusa), found in an FH-heterozygote, consists of a 20 kb deletion spanning from the 5' flanking region to the intron 2 of the LDL-receptor gene. The elimination of the promoter and the first two exons prevents the transcription of the deleted allele, as shown by Northern blot analysis of LDL-R mRNA isolated from the proband's fibroblasts. The second deletion (FH Reggio Emilia), which eliminates 11 nucleotides of exon 10, was also found in an FH heterozygote. The characterization of this deletion was made possible by a combination of techniques such as single strand conformation polymorphism (SSCP) analysis, direct sequence of exon 10 and cloning of the normal and deleted exon 10 from the proband's DNA. The 11 nt deletion occurs in a region of exon 10 which contains three triplets (CTG) and two four-nucleotides (CTGG) direct repeats. This structural feature might render this region more susceptible to a slipped mispairing during DNA duplication. Since this deletion causes a shift of the BamHI site at the 5' end of exon 10, a method has been devised for its rapid screening which is based on the PCR amplification of exon 10 followed by BamHI digestion. FH Reggio Emilia deletion produces a shift in the reading frame downstream from Lys458, leading to a sequence of 51 novel amino acids before the occurrence of a premature stop codon (truncated receptor). However, since RT-PCR failed to demonstrate the presence of the mutant LDL-R mRNA in proband fibroblasts, it is likely that the amount of truncated receptor produced in these cells is negligible.

Occurrence of multiple aberrantly spliced mRNAs of the LDL-receptor gene upon a donor splice site mutation that causes familial hypercholesterolemia (FHBenevento)

A novel point mutation of the LDL-receptor gene was found in an Italian patient with homozygous familial hypercholesterolemia. The SSCP analysis of the promoter and of 16 out of the 18 exons of the LDL-receptor gene was negative, suggesting that the mutation might be located in the region of the gene encompassing exons 14 and 15, a region that had not been amenable to polymerase chain reaction (PCR) amplification from genomic DNA. This region was amplified from cDNA by reverse transcription PCR (RT-PCR). RT-PCR of proband cDNA generated three fragments of 800, 600, and 550 bp, respectively, as opposed to a single 720 bp fragment obtained from control cDNA. The sequence of these fragments showed that: i) in the 800-bp fragment exon 14 continued with the 5' end of intron 15 (90 nucleotides), which in turn was followed by exon 16; ii) in the 600-bp fragment exon 14 was followed by the 5' end of exon 15 (50 nucleotides), which continued with exon 16; iii) in the 550-bp fragment exon 14 joined directly to exon 16. These abnormally spliced mRNAs resulted from a G-->A transition at the +1 nucleotide of intron 15, which changed the invariant GT dinucleotide of the 5' donor splice site. That was associated with the activation of two cryptic donor splice sites in intron 15 and exon 15, respectively, and the use of an alternative splicing leading to the skipping of exon 15. Northern blot analysis showed that the overall content of these aberrantly spliced mRNAs in proband fibroblasts was one-fourth that found in control cells. These abnormally spliced mRNAs are predicted to encode three abnormal receptor proteins: the first would contain an insertion of 30 novel amino acids; the second would be a truncated protein of 709 amino acids; the third would be devoid of the 57 amino acids of the O-linked sugar domain. Ligand blot experiments indicated that the amount of LDL-receptor present in proband's fibroblasts was approximately one-tenth that found in control cells.

Partial duplication of the EGF precursor homology domain of the LDL-receptor protein causing familial hypercholesterolemia (FH-Salerno)

A novel mutation of low density lipoprotein (LDL)-receptor gene was found in an Italian family hypercholesterolemia (FH) patient during a screening of 300 FH patients. The proband as well as her daughter were found to be heterozygotes for the mutation. Binding, internalization, and degradation of 125I-labeled LDL by the proband's fibroblasts were reduced to approximately 50% compared to values found in control cells. DNA analysis by Southern blotting showed that the mutant allele was characterized by an insertion of about 10 kb, which resulted from a duplication of exons 9-14 of the LDL-receptor gene. In addition, Northern blot analysis of the proband's RNA showed, besides the normal sized LDL-receptor mRNA (5.3 kb), an additional mRNA of about 6.2 kb. The junction between exon 14 and the duplicated exon 9 was amplified by polymerase chain reaction (PCR) from the cDNA. The sequence of the amplified fragment showed that exon 14 joined the duplicated exon 9 without changing the reading frame. The derived amino acid sequence indicated that the mutated receptor protein had a partial duplication of the EGF precursor homology domain. Ligand and immunoblotting revealed that proband's fibroblasts contained one-half of the normal amount of LDL-receptor protein (molecular mass 130 kDa) and an abnormally large receptor of approximately 160 kDa. The amount of this abnormal receptor as detected by two monoclonal antibodies (10A2 and 4B3) was found to be approximately 30% that of the normal LDL-receptor present in the same cells.(ABSTRACT TRUNCATED AT 250 WORDS)

A new missense mutation (Cys297-->Phe) of the low density lipoprotein receptor in Italian patients with familial hypercholesterolemia (FHTrieste)

During a survey of the mutations of the low density lipoprotein receptor (LDL-R) gene in Italian patients with familial hypercholesterolemia (FH), we identified a novel point mutation, that creates a new EcoRI site at the 5' end of exon 7, in a heterozygous FH subject (FH-100). The sequence of a cDNA fragment encompassing exon 7 showed the presence of a G-->T transversion in codon 297; this created a new EcoRI site and produced a missense mutation, leading to a Cys297-->Phe substitution in repeat A of the epidermal growth factor (EGF) precursor homology domain of LDL-R. Since the substitution of Cys297 disrupts the intracellular transport of the LDL-R protein, as previously demonstrated by site-directed mutagenesis, we suggest that this mutation is the cause of FH in the FH-100 proband. We screened the DNA of 303 Italian FH patients by amplification of exon 7 from genomic DNA followed by digestion with EcoRI or by Southern blotting. Two individuals (FH-64 and FH-127) were found to be carriers of the Cys297-->Phe mutation. Restriction fragment length polymorphism analysis demonstrated that, in two kindreds (FH-64 and FH-100), the haplotype in linkage with the Cys297-->Phe mutation was the same, suggesting the presence of a common ancestor. The Cys297-->Phe mutation has been designated FHTrieste after the name of the city in Northern Italy from which probands FH-100 and FH-127 originate.

Alternative splicing of mutant LDL-receptor mRNA in an Italian patient with familial hypercholesterolemia due to a partial deletion of LDL-receptor gene (FHPotenza)

An analysis of LDL-receptor gene was performed on an Italian patient with heterozygous familial hypercholesterolemia. Restriction enzyme analysis showed that the proband was heterozygous for a deletion of 4.5 kb spanning the 5' end of exon 13 (45 nucleotide residues) to intron 15. Amplification of genomic DNA, using polymerase chain reaction (PCR), followed by direct sequencing, showed that this deletion was identical to the one reported by Lehrman et al. (1986. Proc. Natl. Acad. Sci. 83: 3679-3683). As only the normal LDL-receptor mRNA was detectable in proband fibroblasts by Northern blot, we used reverse transcription-PCR to amplify the mutant mRNA using primers complementary to exon 6 (sense) and exon 18 (antisense). The amplification of control cDNA resulted in a single fragment of 1725 nucleotides containing the normal sequence. The amplification of cDNA from the proband produced the 1725-nucleotide fragment (as in the control) and three additional fragments (F1, F2, and F3) of smaller size. The direct sequence showed that in the F1 fragment exon 12 was joined to exon 16; in the F2 fragment exon 12 was joined to exon 17; and in the F3 fragment exon 11 was joined to exon 16. Thus, the deletion-bearing allele generated three mRNAs, two of which resulted from alternative splicings leading to the skipping of exons 16 and 12, respectively. It is expected that the translation of these mutant mRNAs will generate three aberrant proteins, the synthesis of which should be negligible in view of the very low content of the corresponding mRNAs.

A large deletion in the LDL receptor gene--the cause of familial hypercholesterolemia in three Italian families: a study that dates back to the 17th century (FH-Pavia)

In the LDL-receptor gene, a large rearrangement causing hypercholesterolemia was detected in three apparently unrelated families living in northern Italy. In all probands, binding, internalization, and degradation of 125I-LDL measured in skin fibroblasts were found to be 40%-50% of control values, indicative of heterozygous familial hypercholesterolemia (FH). Southern blot analysis revealed that the probands were heterozygous for a large (25-kb) deletion of the LDL-receptor gene eliminating exons 2-12. The affected subjects possessed two LDL-receptor mRNA species: one of normal size (5.3 kb) and one of smaller size (3.5 kb). In the latter mRNA, the coding sequence of exon 1 is joined to the coding sequence of exon 13, causing a change in the reading frame and thereby giving rise to a premature stop codon. The receptor protein deduced from the sequence of the defective mRNA is a short polypeptide of 29 amino acids, devoid of any function. Tracing these three families back to the 17th century, we found both their common ancestor and the possible origin of the mutation, in a region which is called "Lomellina" and which is located in southwest Lombardy, near the old city of Pavia. Therefore we named the mutation "FH-Pavia."

Characterization of three mutations of the low density lipoprotein receptor gene in Italian patients with familial hypercholesterolemia

Three gross rearrangements of the low density lipoprotein receptor (LDL-R) gene were recognized during a survey of 23 unrelated Italian subjects with familial hypercholesterolemia (FH). Restriction endonuclease data were obtained by Southern blotting and hybridization with exon-specific probes. Proband FH-29 is heterozygous for a 4-kb deletion, which eliminates exons 13 and 14. This mutation is similar to that previously reported by other investigators in one Italian homozygous and two British and Canadian heterozygous patients. Proband FH-30 is homozygous for a 5.5-kb insertion caused by a duplication of exons 16 and 17 of the LDL-R gene. LDL-R mRNA isolated from skin fibroblasts of FH-30 was found to be larger than normal mRNA (5.6 versus 5.3 kb), in concordance with the insertion of the 236 nucleotides corresponding to exons 16 and 17. Proband FH-44 was found to have greater than 25-kb deletion, which eliminates the first six exons and the promoter region of the gene. This is the first example of a deletion that eliminates the promoter as well as the ligand-binding domain of the LDL-R gene. In the skin fibroblasts of this patient, the level of LDL-R mRNA was approximately half that found in control fibroblasts. We designate the new mutations found in FH-30 and FH-44 as FHviterbo and FHBologna-1, respectively, after the names of the Italian cities where the two patients were born.

Duplication of exons 13, 14 and 15 of the LDL-receptor gene in a patient with heterozygous familial hypercholesterolemia

During a survey of Italian patients with familial hypercholesterolemia (FH), we identified an FH heterozygous patient with a gross rearrangement of the low density lipoprotein (LDL) receptor gene. Southern blot analysis of the proband's DNA digested with restriction enzymes PvuII, BamHI, BglII and XbaI and hybridization with cDNA probes complementary to the 3' end of the gene revealed the presence of abnormal fragments that were approximately 7 kb larger than their normal counterparts. DNA digestion with other enzymes (EcoRV, NcoI, KpnI and StuI) and hybridization with probes complementary to exons 13-17 generated normal fragments and an abnormal fragment of 6.3-6.8 kb. These results are consistent with the presence of an insertion of approximately 7 kb caused by a duplication of exons 13, 14 and 15. This is a novel mutation that is most probably the result of an unequal crossing-over between repetitive sequences located in intron 12 and intron 15. This novel mutation has been designated FHBologna 2.