Genome-wide association study identifies the common variants in CYP3A4 and CYP3A5 responsible for variation in tacrolimus trough concentration in Caucasian kidney transplant recipients

The immunosuppressant tacrolimus (TAC) is metabolized by both cytochrome P450 3A4 (CYP3A4) and CYP3A5 enzymes. It is common for European Americans (EA) to carry two CYP3A5 loss-of-function (LoF) variants that profoundly reduces TAC metabolism. Despite having two LoF alleles, there is still considerable variability in TAC troughs and identifying additional variants in genes outside of the CYP3A5 gene could provide insight into this variability. We analyzed TAC trough concentrations in 1345 adult EA recipients with two CYP3A5 LoF alleles in a genome-wide association study. Only CYP3A4*22 was identified and no additional variants were genome-wide significant. Additional high allele frequency genetic variants with strong genetic effects associated with TAC trough variability are unlikely to be associated with TAC variation in the EA population. These data suggest that low allele frequency variants, identified by DNA sequencing, should be evaluated and may identify additional variants that contribute to TAC pharmacokinetic variability.

Genomewide Association Study of Tacrolimus Concentrations in African American Kidney Transplant Recipients Identifies Multiple CYP3A5 Alleles

We previously reported that tacrolimus (TAC) trough blood concentrations for African American (AA) kidney allograft recipients were lower than those observed in white patients. Subtherapeutic TAC troughs may be associated with acute rejection (AR) and AR-associated allograft failure. This variation in TAC troughs is due, in part, to differences in the frequency of the cytochrome P450 CYP3A5*3 allele (rs776746, expresses nonfunctional enzyme) between white and AA recipients; however, even after accounting for this variant, variability in AA-associated troughs is significant. We conducted a genomewide association study of TAC troughs in AA kidney allograft recipients to search for additional genetic variation. We identified two additional CYP3A5 variants in AA recipients independently associated with TAC troughs: CYP3A5*6 (rs10264272) and CYP3A5*7 (rs41303343). All three variants and clinical factors account for 53.9% of the observed variance in troughs, with 19.8% of the variance coming from demographic and clinical factors including recipient age, glomerular filtration rate, anticytomegalovirus drug use, simultaneous pancreas-kidney transplant and antibody induction. There was no evidence of common genetic variants in AA recipients significantly influencing TAC troughs aside from the CYP3A gene. These results reveal that additional and possibly rare functional variants exist that account for the additional variation.

Genotype-guided tacrolimus dosing in African-American kidney transplant recipients

Tacrolimus is dependent on CYP3A5 enzyme for metabolism. Expression of the CYP3A5 enzyme is controlled by several alleles including CYP3A5*1, CYP3A5*3, CYP3A5*6 and CYP3A5*7. African Americans (AAs) have on average higher tacrolimus dose requirements than Caucasians; however, some have requirements similar to Caucasians. Studies in AAs have primarily evaluated the CYP3A5*3 variant; however, there are other common nonfunctional variants in AAs (CYP3A5*6 and CYP3A5*7) that do not occur in Caucasians. These variants are associated with lower dose requirements and may explain why some AAs are metabolically similar to Caucasians. We created a tacrolimus clearance model in 354 AAs using a development and validation cohort. Time after transplant, steroid and antiviral use, age and CYP3A5*1, *3, *6 and *7 alleles were significant toward clearance. This study is the first to develop an AA-specific genotype-guided tacrolimus dosing model to personalize therapy.

Molecular testing in congenital adrenal hyperplasia due to 21α-hydroxylase deficiency in the era of newborn screening

Newborn screening (NBS) identifies the majority of classical [salt-wasting (SW) and simple-virilizing (SV)] cases of congenital adrenal hyperplasia (CAH) due to 21α-hydroxylase (21α-OHase) during the first days of life. Diagnosis of classical CAH is confirmed by follow-up serum 17-hydroxyprogesterone and/or the adrenocorticotropin stimulation test; however, neither test definitively distinguishes between the classical subtypes. After confirmation, all newborns are started on hydrocortisone (glucocorticoid) and fludrocortisone (mineralocorticoid) treatment. While initiating fludrocortisone treatment in classical CAH patients, independent of subtype and before SW signs or symptoms occur, prevents a life-threatening SW crisis, it may later complicate distinguishing between the classical subtypes. Genotype-phenotype correlations in 21α-OHase deficiency are excellent; however, molecular testing is not a regular part of the diagnostic workup. Molecular testing on 39 patients (25 identified by NBS) with an already established diagnosis of CAH identified 11 SW patients (8 identified by NBS) whose mutations suggested further biochemical and clinical reassessment of their subtype. Overall, SW accounted for 57.6% of our classical CAH patients, below the generally accepted figure that >75% of classical CAH are comprised of the SW form. In the era of NBS, molecular testing is a valuable supplemental tool identifying patients who may benefit from reassessment of their salt-retaining ability.

Pair-wise multifactor dimensionality reduction method to detect gene-gene interactions in a case-control study

OBJECTIVE

The identification of gene-gene interactions has been limited by small sample size and large number of potential interactions between genes. To address this issue, Ritchie et al. [2001] have proposed multifactor dimensionality reduction (MDR) method to detect polymorphisms associated with the disease risk. The MDR reduces the dimension of the genetic factors by classifying them into high-risk and low-risk groups. The strong point in favor of MDR is that it can detect interactions in absence of significant main effects. However, it often suffers from the sparseness of the cells in high-dimensional contingency tables, since it cannot classify an empty cell as high risk or low risk.

METHOD

We propose a pair-wise multifactor dimensionality reduction (PWMDR) approach to address the issue of MDR in classifying sparse or empty cells. Instead of looking at the higher dimensional contingency table, we score each pair-wise interaction of the genetic factors involved and combine the scores of all such pairwise interactions.

RESULTS

Simulation studies showed that the PWMDR generally had greater power than MDR to detect third order interactions for polymorphisms with low allele frequencies. The PWMDR also outperformed the MDR in detecting gene-gene interaction on a kidney transplant dataset.

CONCLUSION

The PWMDR outperformed the MDR to detect polymorphisms with low frequencies.

Molecular basis of type IA (tyrosinase negative) oculocutaneous albinism

Type IA (Tyrosinase negative) oculocutaneous albinism (OCA) is produced by mutations of the tyrosinase gene. We have found a total of 13 different mutations associated with type IA OCA. Analysis of the distribution of the 9 missense mutations shows that most of these mutations cluster in three areas of the gene. All but one of these mutations involve amino acids that are conserved between the mouse and human. Two clusters involve the copper A and copper B binding sites, and could disrupt the metal ion-protein interaction necessary for enzyme function. The third cluster is in exon I and could represent an important functional domain of the enzyme such as the tyrosine binding site. The deletion or insertion frameshift mutations are distributed throughout the coding region and do not appear to cluster. We conclude that a diverse number of mutations are responsible for type IA OCA and many individuals are compound heterozygotes for mutations responsible for this genetic disease (Table 3).

Alternative splicing of the tyrosinase gene transcript in normal human melanocytes and lymphocytes

We have identified and isolated ectopically expressed tyrosinase transcripts in normal human melanocytes and lymphocytes and in a human melanoma (MNT-1) cell line to establish a baseline for the expression pattern of this gene in normal tissue. Tyrosinase mRNA from human lymphoblastoid cell lines was reverse transcribed and amplified using specific "nested" primers. This amplification yielded eight identifiable transcripts; five that resulted from alternative splicing patterns arising from the utilization of normal and alternative splice sequences. Identical splicing patterns were found in transcripts from human primary melanocytes in culture and a melanoma cell line, indicating that lymphoblastoid cell lines provide an accurate reflection of transcript processing in melanocytes. Similar splicing patterns have also been found with murine melanocyte tyrosinase transcripts. Our results demonstrate that alternative splicing of human tyrosinase gene transcript produces a number of predictable and identifiable transcripts, and that human lymphoblastoid cell lines provide a source of ectopically expressed transcripts that can be used to study the biology of tyrosinase gene expression in humans.

Evidence for genetic heterogeneity in families with congenital motor nystagmus (CN)

Congenital motor nystagmus (CN) is a relatively common genetic disorder (approximately 1 in 1500) characterized by bilateral involuntary ocular oscillations, with onset occurring within the first six months of life. To date, three loci associated with CN have been mapped to chromosomes 6p12, Xp11.4-p11.3, and Xq26-q27. We analyzed five pedigrees segregating for CN. Mapping studies using markers in these three regions showed that only one pedigree exhibited suggestive linkage with a lod score of 2.08, straight theta=0.0, at chromosome Xp11. This pedigree had both affected male and female members, with two unaffected obligate female carriers. The remaining four pedigrees did not exhibit evidence of linkage for any of the three chromosome locations. Three of the pedigrees, Pedigrees 2, 4, and 5, exhibited several instances of male-to-male transmission, excluding X-linkage, and exhibited a lod score of -3.82, straight theta=0.0, for marker D6S459 located at 6p12, thus excluding the chromosome 6 locus. This provides evidence for at least a fourth locus associated with CN.

The tyrosinase gene and oculocutaneous albinism type 1 (OCA1): A model for understanding the molecular biology of melanin formation

Through the last century there has been a steady progression in our understanding of the biology of melanin biosynthesis. Much of this work includes the analysis of coat color mutations of the mouse and albinism in man. Our understanding has been greatly enhanced in the last 10 years, as the molecular pathogenesis of albinism has been better understood. Different mutations of the tyrosinase gene (TYR) , and their association with oculocutaneous albinism type 1 (OCA1) has provided insight into the biology of tyrosinase, including protein trafficking and structure/function analysis. Several questions still remain, including cryptic mutations that affect tyrosinase activity and the minimum amount of pigment required for normal optic development. The next 10 years should prove just as exciting as the last.

Molecular basis of albinism: mutations and polymorphisms of pigmentation genes associated with albinism

Albinism, caused by a deficiency of melanin pigment in the skin, hair, and eye (oculocutaneous albinism [OCA]), or primarily in the eye (ocular albinism [OA]), results from mutations in genes involved in the biosynthesis of melanin pigment. The lack of melanin pigment in the developing eye leads to fovea hypoplasia and abnormal routing of the optic nerves. These changes are responsible for the nystagmus, strabismus, and reduced visual acuity common to all types of albinism. Mutations in six genes have been reported to be responsible for different types of oculocutaneous and ocular albinism, including the tyrosinase gene (TYR) and OCA1 (MIM# 203100), the OCA2 gene and OCA2 (MIM# 203200), the tyrosinase-related protein-1 gene (TYRP1) and OCA3 (MIM# 203290), the HPS gene and Hermansky-Pudlak syndrome (MIM# 203300), the CHS gene (CHS1), and Chediak-Higashi syndrome (MIM# 214500), and the X-linked ocular albinism gene and OA1 (MIM#300500). The function of only two of the gene products is known tyrosinase and tyrosinase-related protein-1 both of which are enzymes in the melanin biosynthetic pathway. Continued mutational analysis coupled with function/structure studies should aid our understanding of the function of the remaining genes and their role in albinism. Mutation and polymorphism data on these genes are available from the International Albinism Center Albinism Database web site (http://www.cbc.umn.edu/tad).

Mutations of the human tyrosinase gene associated with tyrosinase related oculocutaneous albinism (OCA1). Mutations in brief no. 204. Online

Mutations in the human tyrosinase gene produce tyrosinase-related oculocutaneous albinism (OCA1, MIM #203100). Tyrosinase is a copper containing enzyme and is responsible for catalyzing the rate limiting step in melanin biosynthesis, the hydroxylation of tyrosine to dopaquinone. We report 13 new mutations in the tyrosinase gene associated with OCA1A (without pigment) and OCA1B (with pigment) including 9 missense mutations (H19Q, R521, R77C, G97R, C289R, L312V, P313R, F340L and H404P), two nonsense mutations (W80X and R116X) and two frameshift mutations (53delG and 223 delG). Our previous work has defined clusters of missense mutations that appear to represent functional domains of the enzyme, and three of the missense mutations fall into these clusters including two (F340L and H404P) that flank the copper B bindng site and the missense mutation R52I that is located in the amino terminal end cluster of the protein. The G97R missense mutation is the first identified within the epidermal growth factor (EGF)-like sequence and the H19Q missense mutation alters the cleavage site of the signal peptide sequence. Mutational analysis can provide a definitive diagnosis of the type of OCA as well as help structure/function analysis.

BRCA1 susceptibility markers and postmenopausal breast cancer: the Iowa Women's Health Study

Much research on early-onset breast cancer families has been performed and has shown that breast cancer in many of these families is linked to either BRCA1 or BRCA2. Fewer studies have examined the role of genetic predisposition in postmenopausal breast cancer. A nested case-control family study of breast cancer was conducted within the Iowa Women's Health Study, a population-based prospective study of 41,836 postmenopausal women. Probands were 251 incident cases diagnosed between 1988 and 1989. Three-generation pedigrees were developed through mailed questionnaires. From this collection of pedigrees, thirteen were identified for more detailed genetic analysis. Sibling-pair linkage analyses were performed using polymorphic markers in candidate regions in these 13 families with multiple cases of breast and other cancers. Four of the DNA markers are located on chromosome 17, and two of these (D17S579 and THRA1) flank the BRCA1 locus. Significant evidence for linkage to D17S579 was obtained in the total sample, in a model without inclusion of covariates or age at onset (P = 0.005), and in a model adjusted for five measured covariates and for variable age at onset (P = 0.008). Complete sequencing of the BRCA1 gene in these families, including all intron/exon boundaries, failed to reveal any mutations in 24 women with breast cancer from the 13 families. These data suggest that in some families identified by postmenopausal breast cancer cases, breast cancer risk may be mediated by a gene (or genes) in the BRCA1 region, but not BRCA1 itself.

Gene expression analysis

The response of cells to extracellular signals usually requires altered expression of many genes, possibly including several distinct metabolic pathways. In some cases, only a subset of genes involved in such responses are known, which requires techniques to analyze changes in the expression of multiple genes, both known and unknown. Three techniques, two-dimensional gel electrophoresis, differential display, and gene discovery arrays, provide opportunities for measuring changes in gene expression levels, as well as for identifying novel gene products.

Albinism

Albinism was one of the first genetic diseases to be noted in humans, but until relatively recently, little was known of the molecular mechanisms involved in its pathogenesis. Recent advances have shown us that mutations in at least seven different genes can cause a reduction in melanin pigment biosynthesis, producing the various associated clinical features associated with albinism, including hypopigmentation of the skin, hair, and eyes; optic track misrouting; foveal hypoplasia; and reduced visual acuity. Analysis of mutations in these seven genes has revealed that the phenotypic spectrum associated with albinism is broad, making molecular analysis an important part in the accurate diagnosis of this disease.

Fifty-year follow-up of cancer incidence in a historical cohort of Minnesota breast cancer families

A family history of breast cancer is well established as a risk factor for the disease. Because family history is a dynamic rather than a static characteristic, longitudinal studies of entire families can be very instructive in quantifying the significance of risk classification. The Minnesota Breast Cancer Family Study is a historical cohort study of relatives of a consecutive series of 426 breast cancer cases (probands) identified between 1944 and 1952. The incidence of cancer and the measurement of risk factors in sisters, daughters, granddaughters, nieces, and marry-ins was determined through telephone interviews and mailed questionnaires. Ninety-eight percent of eligible families were recruited, and 93% of members participated. A total of 9073 at-risk women were studied: 56% were biological relatives of the case probands, whereas the others were related through marriage. Through 1996, 564 breast cancers were identified in nonprobands. Compared to the rate of breast cancer among marry-ins (188 cases), sisters and daughters of the probands were at a 1.9-fold greater age-adjusted risk (128 cases; 95% confidence interval, 1.4-2.4); granddaughters and nieces were at a 1.5-fold greater risk (248 cases, 95% confidence interval, 1.2-1.8). The breast cancer risk since 1952 was not distributed equally across families: although all biological relatives had a family history of breast cancer, 166 families (39%) experienced no additional cases. Most of the cases occurred among a subset of families: 21 families had 5 breast or ovarian cancers, 8 had 6, 2 had 7, and 4 had > or =8. There was no evidence of significantly increased risk for cancer at other sites, including the ovaries, cervix, uterus, colon, pancreas, stomach, or lymphatic tissue, although there was some evidence that stomach cancer in previous generations may help define the susceptible subset. These families contain four to five generations of validated occurrences of cancer, thus minimizing the uncertainty of genetic risk inherent in a disease with a late and variable age at onset. The patterns of breast cancer in these multigeneration families is consistent with the influence of autosomal dominant susceptibility in a subset, low penetrance genes in another, and purely environmental influences in the remainder.

Microphthalmia-associated transcription factor (MITF) locus lacks linkage to human vitiligo or osteopetrosis: an evaluation

The microphthalmia-associated transcription factor (MITF) locus has been mapped to human chromosome 3p12-p14.1, and encodes a basic helix-loop-helix zipper (bHLH-ZIP) protein homologous to a number of transcription factors. Numerous mutations at the mouse microphthalmia (mi) locus have been described, and all have reduced or absent pigmentation of the eyes, ears, and/or pelage, with some genotypes exhibiting small or absent eyes and osteopetrosis. The mivit/vit mutation at the mouse mi locus produces a postnatal depigmentation that resembles human vitiligo. The mice homozygous for this mi allele show a progressive loss of cutaneous, hair and ocular pigmentation with age. Vitiligo, an acquired depigmentary disorder, is characterized by patchy depigmentation of skin that generally begins around puberty and tends to become more progressive over time. There is suggestive evidence that human vitiligo may be inherited; however, the mode of inheritance is still debated and the pathogenesis is not clearly delineated. The human disorder osteopetrosis is characterized by a generalized net accumulation of skeletal mass and results from reduced osteoclast function in the bone. This is an inherited disorder and has been associated with mi in a mutant mouse. Therefore, the possible involvement of the MITF locus in the pathogenesis of either familial vitiligo or osteopetrosis was investigated. Linkage analysis was performed using microsatellite polymorphic markers D3S2465, D3S1261, and D3S1766 on genomic DNA from 26 families with vitiligo/osteopetrosis. D3S1261 is physically located at or near the MITF locus, while D3S2465 and D3S1766 are flanking the locus at about 17.5 cM genetic distance each side. Evidence from LOD score analysis surprisingly indicated that none of the families with vitiligo or osteopetrosis are linked to these short tandem repeat polymorphisms (STRPs). Thus, the human homolog (MITF) of the mouse mi gene, a good candidate gene at the phenotypic level, may not be involved in the pathogenesis of familial human vitiligo or osteopetrosis.

Molecular analysis of an extended Palestinian family from Israel with monilethrix

We describe the molecular analysis of a large three generation Palestinian family segregating for monilethrix. Previous reports have shown that mutations in type-II hair cortex keratin genes, hHb1 and hHb6, are associated with monilethrix. Genetic linkage analysis performed on this family using markers flanking the hHb6 gene exhibited strong evidence for linkage. Sequence analysis revealed a nucleotide substitution of G --> T at nucleotide 1230 resulting in a glutamic acid to aspartic acid amino acid substitution at codon 410, identical to that reported in a French family. The family in our study provides further evidence that mutations of the hHb6 gene are responsible for monilethrix.

Multiplexed short tandem repeat polymorphisms of the Weber 8A set of markers using tailed primers and infrared fluorescence detection

Short tandem repeat polymorphism (STRP) markers have become important reagents for mapping genetic diseases. These markers are available as screening sets, which are located in all chromosomes at discrete intervals, allowing the entire genome to be analyzed. Mapping studies that include many individuals in the analysis necessitate the production of large numbers of genotypes. In an effort to increase the efficiency and lower the cost of using these STRP screening sets, we have divided the amplification primers of the Weber 8A screening set into groups that can be amplified in single polymerase chain reaction (PCR) amplification reactions, resulting in a reduction of both time and cost. Fluorescently-labeled amplification products were produced using a three primer reaction. The forward STRP amplification primer for each marker contained a 19 bp sequence at the 5' end. A fluorescently-labeled primer, with a sequence identical to the 19 bp tail, was added to the amplification reaction as the sole source of fluorescent label. The STRP banding pattern is detected using an automated fluorescent DNA sequencer. Use of this multiplexed genomic screening set should greatly enhance the mapping of human disease loci.

A second locus for familial high myopia maps to chromosome 12q

Myopia, or nearsightedness, is the most common eye disorder worldwide. "Pathologic" high myopia, or myopia of <=-6.00 diopters, predisposes individuals to retinal detachment, macular degeneration, cataract, or glaucoma. A locus for autosomal dominant pathologic high myopia has been mapped to 18p11.31. We now report significant linkage of high myopia to a second locus at the 12q21-23 region in a large German/Italian family. The family had no clinical evidence of connective-tissue abnormalities or glaucoma. The average age at diagnosis of myopia was 5.9 years. The average spherical-component refractive error for the affected individuals was -9.47 diopters. Markers flanking or intragenic to the genes for the 18p locus, Stickler syndromes type I and II (12q13.1-q13.3 and 6p21.3), Marfan syndrome (15q21.1), and juvenile glaucoma (chromosome 1q21-q31) showed no linkage to the myopia in this family. The maximum LOD score with two-point linkage analysis in this pedigree was 3.85 at a recombination fraction of .0010, for markers D12S1706 and D12S327. Recombination events identified markers D12S1684 and D12S1605 as flanking markers that define a 30.1-cM interval on chromosome 12q21-23, for the second myopia gene. These results confirm genetic heterogeneity of myopia. The identification of this gene may provide insight into the pathophysiology of myopia and eye development.

Evidence that a locus for familial high myopia maps to chromosome 18p

Myopia, or nearsightedness, is the most common human eye disorder. A genomewide screen was conducted to map the gene(s) associated with high, early-onset, autosomal dominant myopia. Eight families that each included two or more individuals with >=-6.00 diopters (D) myopia, in two or more successive generations, were identified. Myopic individuals had no clinical evidence of connective-tissue abnormalities, and the average age at diagnosis of myopia was 6.8 years. The average spherical component refractive error for the affected individuals was -9.48 D. The families contained 82 individuals; of these, DNA was available for 71 (37 affected). Markers flanking or intragenic to the genes for Stickler syndrome types 1 and 2 (chromosomes 12q13.1-q13.3 and 6p21.3, respectively), Marfan syndrome (chromosome 15q21.1), and juvenile glaucoma (chromosome 1q21-q31) were also analyzed. No evidence of linkage was found for markers for the Stickler syndrome types 1 and 2, the Marfan syndrome, or the juvenile glaucoma loci. After a genomewide search, evidence of significant linkage was found on chromosome 18p. The maximum LOD score was 9.59, with marker D18S481, at a recombination fraction of .0010. Haplotype analysis further refined this myopia locus to a 7.6-cM interval between markers D18S59 and D18S1138 on 18p11.31.

Identification of a novel transcript produced by the gene responsible for the Hermansky-Pudlak syndrome in Puerto Rico

Hermansky-Pudlak Syndrome (HPS) is a rare, autosomal recessive disorder that is characterized by oculocutaneous albinism, a predisposition to mild bleeding caused by storage-pool deficient platelets, and a ceroid storage disorder. A gene responsible for HPS in Puerto Rico maps to chromosome 10q2 and isolation of the gene has been reported. We have now identified a variant HPS cDNA that contains the same 5' sequence as the published HPS gene and a unique 3' sequence. Analysis of genomic DNA suggests that the two cDNA are derived from alternative transcripts of a single gene; two polyadenylated transcripts were found in normal human melanocytes, human bone marrow cells, human melanoma cells, lymphoblastoid cell lines, and megakaryocytic leukemia cells by reverse transcriptase polymerase chain reaction and northern analysis. The splicing exhibited by this gene is identical to the splicing found to produce two alternative transcripts of the Chediak-Higashi Syndrome gene, another pigment disorder exhibiting platelet storage pool deficiency. These studies show that the HPS gene on chromosome 10 is complex and may have more than one biologically active transcript.

The clinical spectrum of albinism in humans

Oculocutaneous albinism is characterized by a congenital reduction or absence of melanin pigment in the skin, hair and eyes. The reduction in the hair and skin results in a change in color but no change in the development or function of these tissues, while the absence of melanin pigment in the eye leads to abnormal development and function. Of particular interest are mutations that are associated with a slow accumulation of pigment in the hair and eyes over time, while retaining the ocular defects of albinism. Analysis of these mutations might provide the insight that we need to understand the interaction between the pigment system and the development of the optic system.

Mutation in and lack of expression of tyrosinase-related protein-1 (TRP-1) in melanocytes from an individual with brown oculocutaneous albinism: a new subtype of albinism classified as "OCA3"

Most types of human oculocutaneous albinism (OCA) result from mutations in the gene for tyrosinase (OCA1) or the P protein (OCA2), although other types of OCA have been described but have not been mapped to specific loci. Melanocytes were cultured from an African-American with OCA, who exhibited the phenotype of Brown OCA, and his normal fraternal twin. Melanocytes cultured from the patient with OCA and the normal twin appeared brown versus black, respectively. Melanocytes from both the patient with OCA and the normal twin demonstrated equal amounts of NP-40-soluble melanin; however, melanocytes from the patient with OCA contained only 7% of the amount of insoluble melanin found from the normal twin. Tyrosinase- related protein-1 (TRP-1) was not detected in the OCA melanocytes by use of various anti-TRP-1 probes. Furthermore, transcripts for TRP-1 were absent in cultured OCA melanocytes. The affected twin was homozygous for a single-bp deletion in exon 6, removing an A in codon 368 and leading to a premature stop at codon 384. Tyrosine hydroxylase activity of the OCA melanocytes was comparable to controls when assayed in cell lysates but was only 30% of controls when assayed in intact cells. We conclude that this mutation of the human TRP-1 gene affects its interaction with tyrosinase, resulting in dysregulation of tyrosinase activity, promotes the synthesis of brown versus black melanin, and is responsible for a third genetic type of OCA in humans, which we classify as "OCA3."

Diagnosis of oculocutaneous albinism with molecular analysis

PURPOSE

To use molecular analysis to diagnose oculocutaneous albinism in a patient with an atypical clinical presentation.

METHODS

A 34-year-old woman with a history of strabismus and absent cutaneous pigment underwent comprehensive ophthalmic examination, visual-evoked potentials to detect altered optic decussation, and molecular analysis.

RESULTS

Examination showed fine nystagmus, iris transillumination, foveal hypoplasia, and corrected visual acuity of 20/25 in each eye. Misrouting of the retinostriate fibers was demonstrated with visual-evoked potentials. Mutations in the tyrosinase gene established the diagnosis of oculocutaneous albinism 1 even though the patient had atypical clinical features.

CONCLUSIONS

Molecular analysis can establish the diagnosis of oculocutaneous albinism 1 in the patient with atypical ocular features.

Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers

The use of short tandem repeat polymorphisms (STRPs) as marker loci for linkage analysis is becoming increasingly important due to their large numbers in the human genome and their high degree of polymorphism. Fluorescence-based detection of the STRP pattern with an automated DNA sequencer has improved the efficiency of this technique by eliminating the need for radioactivity and producing a digitized autoradiogram-like image that can be used for computer analysis. In an effort to simplify the procedure and to reduce the cost of fluorescence STRP analysis, we have developed a technique known as multiplexing STRPs with tailed primers (MSTP) using primers that have a 19-bp extension, identical to the sequence of an M13 sequencing primer, on the 5' end of the forward primer in conjunction with multiplexing several primer pairs in a single polymerase chain reaction (PCR) amplification. The banding pattern is detected with the addition of the M13 primer-dye conjugate as the sole primer conjugated to the fluorescent dye, eliminating the need for direct conjugation of the infrared fluorescent dye to the STRP primers. The use of MSTP for linkage analysis greatly reduces the number of PCR reactions. Up to five primer pairs can be multiplexed together in the same reaction. At present, a set of 148 STRP markers spaced at an average genetic distance of 28 cM throughout the autosomal genome can be analyzed in 37 sets of multiplexed amplification reactions. We have automated the analysis of these patterns for linkage using software that both detects the STRP banding pattern and determines their sizes. This information can then be exported in a user-defined format from a database manager for linkage analysis.

A gene causing Hermansky-Pudlak syndrome in a Puerto Rican population maps to chromosome 10q2

Hermansky-Pudlak syndrome (HPS) is an autosomal recessive disorder that affects pigment production and platelet function and causes the deposition of a ceroid-like material in various tissues. Variability in the phenotype and the presence of several potential mouse models suggest that HPS may be a heterogeneous disorder. In order to identify a gene responsible for HPS, we collected blood samples from a relatively homogeneous population in Puerto Rico where the HPS carrier frequency is estimated to be 1 in 21. Analysis of pooled DNA samples allowed us to rapidly screen the genome for candidate loci, and significant evidence for linkage was detected for a marker on chromosome 10q. This region of the human genome is conserved syntenically with the region on mouse chromosome 19 where two possible mouse models for HPS, pale ear and ruby eye, are located. This linkage result was verified with additional markers, and a maximum LOD score of 5.07 at theta = .001 was calculated for marker D10S198. Haplotype analysis places the HPS gene in a region of approximately 14 cM that contains the markers D10S198 and D10S1239.

Detection of a Tsp509I polymorphism in the 3' UTR of the human tyrosinase related protein-1 (TYRP) gene

We have identified a Tsp509I polymorphism in the 3' UTR of the human tyrosinase related protein-1 gene (TYRP). TYRP is one of several genes involved in melanin pigment production.

Molecular basis of oculocutaneous albinism

Oculocutaneous albinism (OCA) is a complex group of genetic disorders that have historically been defined by clinical and biochemical methods. Recent advances in the molecular biology of pigmentation have greatly increased our understanding of the complexity of this group of disorders. To date, two different types of OCA (OCA1 and OCA2) have been mapped to specific chromosomal regions. Mutations have been found in the tyrosinase locus associated with OCA1 and the human homologue to the murine pink-eyed dilution locus associated with OCA2. Analysis of these genes and their mutations will allow us to better define and categorize the different types of albinism. Further, the analysis of these genes and their mutations will provide information on the role of these gene products in melanin biosynthesis and the effect specific mutations have on the pathogenesis of albinism.

Analysis of tyrosinase mutations associated with tyrosinase-related oculocutaneous albinism (OCA1)

Mutations of the tyrosinase gene associated with a partial or complete loss of enzymatic activity are responsible for tyrosinase related oculocutaneous albinism (OCA1). A large number of mutations have been identified and their analysis has provided insight into the biology of tyrosinase and the pathogenesis of these different mutations. Missense mutations produce their effect on the activity of an enzyme by altering an amino acid at a specific site. The location of these mutations in the peptide can be used to indicate potential domains important for enzymatic activity. Missense mutations of the tyrosinase polypeptide cluster in four regions, suggesting that these are important functional domains. Two of the potential domains involve the copper binding sites while the others are likely involved in substrate binding. More critical analysis of the copper binding domain of tyrosinase can be gained by analyzing the structure of hemocyanin, a copper-binding protein with a high degree of homology to tyrosinase in the copper binding region. This analysis indicates a single catalytic site in tyrosinase for all enzymatic activities.

Analysis of tyrosinase gene mutations using direct automated infrared fluorescence DNA sequencing of amplified exons

The ability to correctly diagnose the molecular cause of genetic diseases is becoming increasingly important in medicine. This requires an efficient method for the analysis of the DNA sequence of specific genes and the detection of mutations in affected individuals. We report a method to determine the mutations responsible for tyrosinase related albinism (OCA1) using a combination of polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) analysis and direct DNA cycle sequencing using fluorescently labeled oligonucleotides and an automated DNA sequencer based on infrared fluorescence technology. This method allows DNA from several individuals to be sequenced quickly and simultaneously so that the specific location of each mutation and the carrier status of family members can be determined.

Evolution of the tyrosinase related gene (TYRL) in primates

Tyrosinase is the major enzyme responsible for the formation of melanin pigment and is found throughout the animal kingdom. In humans, the tyrosinase gene (TYR) maps to the long arm of chromosome 11 at band q14-->q21, while a tyrosinase related gene (TYRL) maps to the short arm of chromosome 11 at p11.2-->cen. We and others have found that the TYRL locus contains sequences that are similar to exons IV and V of the authentic tyrosinase gene but lacks sequences of exons I, II, and III. In an attempt to understand the evolution of the human tyrosinase gene, we have analyzed TYR and TYRL in primates and have found that exons IV and V of the chimpanzee and gorilla TYR are very similar to the human, with the gorilla sequence being more similar than the chimpanzee. We have also found that the gorilla but not the chimpanzee contains a TYRL locus similar to the human TYRL locus.

Molecular basis of type I (tyrosinase-related) oculocutaneous albinism: mutations and polymorphisms of the human tyrosinase gene

Type I (tyrosinase related) oculocutaneous albinism (OCA) results from mutations of the tyrosinase gene on chromosome 11q that lead to reduced or absent melanin pigment synthesis. The phenotype of Type I OCA is broad, ranging from a total lack to only a moderate reduction of melanin, and the phenotypic variation is associated with different mutant alleles at the tyrosinase locus. A total of 36 mutations have been identified in Type I OCA including 24 missense, 4 nonsense, and 8 frameshift mutations. The majority of affected individuals have been compound heterozygotes with different maternal and paternal alleles. Six polymorphic sites for haplotype analysis have been identified in the tyrosinase gene including 2 in the promoter region, 2 in the coding region associated with alternative amino acids in the protein, and 2 RFLPs in the first intron.

A frequent tyrosinase gene mutation associated with type I-A (tyrosinase-negative) oculocutaneous albinism in Puerto Rico

We have determined the mutations in the tyrosinase gene from 12 unrelated Puerto Rican individuals who have type I-A (tyrosinase-negative) oculocutaneous albinism (OCA). All but one individual are of Hispanic descent. Nine individuals were homozygous for a missense mutation (G47D) in exon I at codon 47. Two individuals were heterozygous for the G47D mutation, with one having a missense mutation at codon 373 (T373K) in the homologous allele and the other having an undetermined mutation in the homologous allele. One individual with negroid features was homozygous for a nonsense mutation (W236X). The population migration between Puerto Rico and the Canary Islands is well recognized. Analysis of three individuals with OCA from the Canary Islands showed that one was a compound heterozygote for the G47D mutation and for a novel missense mutation (L216M), one was homozygous for a missense mutation (P81L), and one was heterozygous for the missense mutation P81L. The G47D and P81L missense mutations have been previously described in extended families in the United States. Haplotypes were determined using four polymorphisms linked to the tyrosinase locus. Haplotype analysis showed that the G47D mutation occurred on a single haplotype, consistent with a common founder for all individuals having this mutation. Two different haplotypes were found associated with the P81L mutation, suggesting that this may be either a recurring mutation for the tyrosinase gene or a recombination between haplotypes.

Analysis of mutations in the copper B binding region associated with type I (tyrosinase-related) oculocutaneous albinism

Mutations of the tyrosinase gene are responsible for type I (tyrosinase-related) oculocutaneous albinism (OCA), an autosomal recessive genetic syndrome with a broad phenotypic spectrum. Mutant tyrosinase alleles can be associated with no melanin synthesis (I-A, tyrosinase-negative OCA), small to moderate amounts of melanin (I-B, yellow OCA) or unusual pigment patterns (I-TS, temperature-sensitive OCA). A total of 26 mutations of this gene have been described in type I OCA. Analysis of all known mis-sense mutations (n = 17) shows that most cluster in three areas of the coding region. Two clusters involve the copper A or copper B binding sites and may disrupt the metal ion-protein interaction necessary for enzyme function and the third cluster is located in exon I. Computer modeling of the secondary structure of the copper binding regions based on homology with the known crystal structure of hemocyanin show that they both consist of two alpha helices containing three histidine ligands that complex to a single copper atom. Mutations in the copper B binding region lie in the region between the two alpha helices that consists of a loop structure. These mutations may affect tyrosinase activity by either altering the position of the alpha helical domains and thus preventing proper copper binding to the histidine ligands, or affecting a catalytic or substrate binding site located between the two alpha helical domains.

Molecular analysis of type I-A (tyrosinase negative) oculocutaneous albinism

Type I oculocutaneous albinism (OCA) is caused by the reduction in or absence of activity of tyrosinase in melanocytes in skin, hair, and the eyes, the result of mutations of the tyrosinase gene. To date, a total of 22 unique mutations in the coding region of tyrosinase have been described in the literature. In this report we present 5 additional mutations of the tyrosinase gene associated with type I-A OCA in four individuals, including 2 missense, 1 frameshift and 2 nonsense mutations, and review the relevant literature on all published mutations. Analysis of the distribution of all identified missense mutations (n = 17) shows that most cluster in three areas of the gene and involve amino acids conserved between humans and the mouse. Two clusters involve the copper A and copper B binding sites and may disrupt the metal ion-protein interaction necessary for enzyme function. The third cluster in exon I could represent a functional domain important in enzyme function such as the tyrosine or the dihydroxyphenylalanine (DOPA) binding site of the enzyme. Small deletions or insertions resulting in frameshift mutations and nonsense mutations are distributed throughout the coding region and do not appear to cluster.

Three different frameshift mutations of the tyrosinase gene in type IA oculocutaneous albinism

Mutations in the gene for the pigment-producing enzyme tyrosinase are responsible for type IA (tyrosinase-negative) oculocutaneous albinism (OCA). Most reported mutations have been single base substitutions. We now report three different frameshift mutations in three unrelated individuals with type IA OCA. The first individual has a single base deletion within a series of five guanidines, resulting in a premature stop codon in exon I on one allele and a missense mutation at codon 382 in exon III on the homologous allele. The second individual is a genetic compound of two separate frameshift mutations, including both the same exon I single base deletion found in the first individual and a deletion of a thymidine-guanidine pair, within the sequence GTGTG, forming a termination codon (TAG) in exon I on the homologous allele. The third individual has a single base insertion in exon I on one allele and a missense mutation at codon 373 in exon III on the homologous allele. The two missense mutations occur within the copper Bbinding region and may interfere with either copper binding to the enzyme or oxygen binding to the copper. These five different mutations disrupt tyrosinase function and are associated with a total lack of melanin biosynthesis.

Molecular analysis of an extended family with type IA (tyrosinase-negative) oculocutaneous albinism

We have analyzed the tyrosinase coding region of three individuals having Type IA OCA within an extended family using genomic DNA amplification and dideoxy sequencing. Two of the affected individuals are dizygotic twins. All three have a common missense mutation at codon 81 (Pro----Leu) within exon I. The twins have a second missense mutation at codon 371 (Asn----Thr) within exon III and the third individual has a second missense mutation at codon 47 (Gly----Asp) within exon I. For each of these three individuals, the loss of enzyme function is the result of two different mutations, showing that they are compound heterozygotes of two mutant tyrosinase alleles.

Non-random distribution of missense mutations within the human tyrosinase gene in type I (tyrosinase-related) oculocutaneous albinism

Type I oculocutaneous albinism (OCA) is produced by mutations of the tyrosinase gene. We report four new missense mutations in the tyrosinase gene in patients with type IA OCA. Three of these mutations occur within exon I and the fourth mutation within exon IV. Analysis of the distribution of these four missense mutations and 12 previously reported missense mutations shows that most cluster in four areas of the gene. Two clusters involve the copper A and copper B binding sites and could disrupt the metal ion-protein interaction necessary for enzyme function. The other two clusters are in exon I and exon IV and could represent important functional domains of the enzyme. We conclude that analysis of the tyrosinase missense mutations will provide insight into the structure-function relationship of this enzyme.

Production and secretion of the 21-23.5 kDa prolactin-like molecules

We recently described the presence of a series of prolactin (PRL)-like molecules (PLMs) in the rat pituitary gland and showed that their formation was not due to artifactual proteolysis of 24 kDa PRL during extraction or to degradation of PRL in lysosomes. In this study we have found (1) in vitro translation of pituitary cell RNA to result in the production of only 24 kDa monomer isoform 2 and no PLMs, (2) that secretion of newly synthesized PLMs is differently regulated than at least a proportion of newly synthesized monomers, (3) that secretion of newly synthesized PLMs occurs after at least a 6 h delay, (4) that cysteamine (a) inhibits the release of the PLMs, (b) causes an increase in their amount versus isoform 2, and (c) causes an intracellular accumulation of pleiomorphic, immature secretory granules, and (5) that cells grown under degranulating culture conditions do not contain PLMs. These results, using normal anterior pituitary cells in primary culture, demonstrate the potential for differential release of the PLMs versus monomer PRL in vivo and are consistent with the production of the PLMs from 24 kDa monomer isoform 2 during secretory granule condensation.

Differential isoform distribution between stored and secreted prolactin

PRL exists within the mammotroph population in a number of different molecular forms. Three of these forms are best described as isoforms, as they have the same mol wt (24K) but differ in their net molecular charges. In this study we have examined the relative proportions of newly synthesized isoforms found in stored (intracellular) vs. secreted (extracellular) PRL. Dissociated cells from female rat anterior pituitaries were cultured for 48 h and then incubated in [35S]methionine (6 h; 37 C). Intracellular and medium proteins were then extracted and resolved by one- and two-dimensional polyacrylamide gel electrophoresis, followed by silver staining or autoradiography. Control experiments, in which biosynthetically labeled PRL was re-extracted, ensured that the isolation conditions did not in themselves promote isoform interconversion. The relative proportions of the PRL isoforms were determined by densitometric scanning of developed autoradiograms. In the cell extracts, the relative proportions were 13.6 +/- 2.1% isoform 1 (least negatively charged), 71.5 +/- 3.26% isoform 2, and 14.7 +/- 1.9% isoform 3 (most negatively charged). In the medium, the relative proportions were 60 +/- 2.89% isoform 1, 20 +/- 1.75% isoform 2, and 11 +/- 1.14% isoform 3. When the labeling was performed in the presence of 0.5 mM cysteamine (an agent we show to distinguish between newly synthesized and older stored hormone and, hence, between the previously described functional subpopulations of mammotrophs), the same ratios of newly synthesized isoforms were secreted from the cells. We conclude that secretion of the different isoforms is more complex than simple proportional release of each form, and based on the cysteamine results, this nonproportional release cannot be attributed to release of one isoform per functional subpopulation of mammotrophs.

Phosphorylation of prolactin

Rat prolactin exhibits microheterogeneity when examined in electrophoretic systems, running as three isoforms having the same molecular weight but different net charges (prolactins 1, 2, and 3 with isoform 3 being the most acidic). As there is precedent for the phosphorylation of a pituitary hormone and phosphorylation is a common cause of microheterogeneity, we examined the possibility that rat prolactin existed in differentially phosphorylated forms. The investigation included examinations of rat prolactin phosphorylation both in vitro and in vivo. For the in vitro studies, purified rat prolactin was incubated with [gamma-32P]ATP and low levels of each of five purified protein kinases. Phosphorylated rat prolactin was identified by autoradiography of silver-stained one- and two-dimensional gels. For the in vivo studies, rat anterior pituitary cells in primary culture were incubated in the presence of H3 32PO4 for 2 or 12 h, after which time the proteins were extracted from the cells, cold acetone-precipitated, or immunoprecipitated and run on two-dimensional gels. We report the in vitro phosphorylation of rat prolactin by cAMP-dependent protein kinase, casein kinase I, protease-activated kinase I, and the calcium/phospholipid-dependent kinase, that phosphorylation with these kinases results in phosphate incorporation only into isoforms 2 and 3, and the phosphorylation of prolactin in rat pituitary cells in primary culture.

Intracellular processing of prolactin

PRL has been reported to exist as a number of mol wt and charge variants. We have attempted to determine the relationships among the charge and lower mol wt variants by two-dimensional gel analysis of pituitary and pituitary cell extracts. Silver-stained gels of the extracts showed three major charge isoforms of 24,000 mol wt PRL (PRLs 1, 2, and 3, with PRL 3 being the most anodic) and what appeared to be an arc of products originating in the region of PRL 3. Each spot in the arc was distinct and represented a small decrease in size (two to eight residues), with a corresponding increase in net negative charge. When primary cell cultures were labeled with [35S] methionine, the three PRL isoforms and arc products were detectable by autoradiography. Western blots of the two-dimensional gels showed the arc products to be immunologically related to PRL. Treatment of the cell cultures with hydroxynorvaline (5 mM), which inhibits processing of pre-PRL to PRL, resulted in doublet spots in the arc. Elimination of protease inhibitors or an increase in temperature during protein isolation had no effect on the relative concentrations of PRL and arc products. Inclusion of standard PRL or [125I]iodo-PRL in the extraction solution did not increase the size of the spots in the arc or produce labeled arc products, respectively. Treatment of the cell cultures with chloroquine (10(-5) M) before and during radiolabeling had no effect on the production of radiolabeled arc products. Analysis of cell culture medium showed at least some of the arc products to be secreted. We conclude that PRL or a PRL-like molecule is processed intracellularly into a number of smaller derivatives. As the arc products accumulate within the cell and are secreted, we suggest that they may be biologically important relatives of PRL.

C pigment locus mutants of the fowl produce enzymatically inactive tyrosinase-like molecules

Three albino mutants of the fowl were tested for tyrosinase activity. Two of these mutants (c and ca) are alleles at the autosomal C locus, while the third mutant (sal) is sex-linked. Both the standard type, E, and sal are tyrosinase positive whereas the two C mutants are tyrosinase negative. Anti-chicken tyrosinase mouse serum was produced and all four genotypes were found to have cross-reacting material to this antiserum. Tyrosinase from the standard type was isolated and its location on denaturing two-dimensional gels determined. A co-migrating series of spots was found within the protein pattern of both the standard type and the tyrosinase positive albino, sal. The same pattern of spots was also observed for c and ca with no apparent change in either the pI or the molecular weight. Transmembrane blots also showed spots that reacted with anti-tyrosinase serum in all four genotypes and that migrated to the same location as that of standard tyrosinase. It is proposed that both c and ca are CRM+ mutants which produce tyrosinase-like molecules that are inactive due to a change that is electrophoretically and antigenically "silent".

Mammotroph autoregulation: uptake of secreted prolactin and inhibition of secretion

A dissociated preparation of normal adult rat pituitary cells has been used to study PRL autoregulation at the level of the mammotroph . Female rat pituitary cells previously cultured for 48 h on polylysine-coated petri dishes were washed to remove serum and accumulated PRL and then incubated in fresh medium in the absence or presence of increasing concentrations of rat PRL. Accurate balance sheets, allowing for degradation and nonspecific adsorption of PRL, showed exogenous PRL to regulate the amount of PRL released by the cells. That this regulation was partly produced by uptake of secreted PRL from the medium was demonstrated by supplementing the medium with [125I]iodo-rat PRL. Inhibition of secretion also played a role and was implied by experiments showing that ease of reversal of the inhibition was inversely proportional to the density of cell culture, which was itself proportional to the amount of PRL in the medium and the duration of autoregulation. These results indicate that normal adult rat pituitary cells in primary culture are capable of regulating the amount of PRL in their external milieu and that uptake of already secreted PRL is an important component of the regulatory mechanism.