Application of microdroplet PCR for large-scale targeted bisulfite sequencing.

Cytosine methylation of DNA CpG dinucleotides in gene promoters is an epigenetic modification that regulates gene transcription. While many methods exist to interrogate methylation states, few current methods offer large-scale, targeted, single CpG resolution. We report an approach combining bisulfite treatment followed by microdroplet PCR with next-generation sequencing to assay the methylation state of 50 genes in the regions 1 kb upstream of and downstream from their transcription start sites. This method yielded 96% coverage of the targeted CpGs and demonstrated high correlation between CpG island (CGI) DNA methylation and transcriptional regulation. The method was scaled to interrogate the methylation status of 77,674 CpGs in the promoter regions of 2100 genes in primary CD4 T cells. The 2100 gene library yielded 97% coverage of all targeted CpGs and 99% of the target amplicons.

Common TMPRSS6 mutations and iron, erythrocyte, and pica phenotypes in 48 women with iron deficiency or depletion.

BACKGROUND: TMPRSS6 A736V is associated with lower transferrin saturation (TS), hemoglobin (Hb), and mean corpuscular volume (MCV) levels in general adult populations. We sought to identify relationships of TMPRSS6 K253E, A736V, and Y739Y to iron, erythrocyte, and pica phenotypes in women with iron deficiency or depletion. METHODS: We tabulated observations on 48 outpatient non-pregnant women who had iron deficiency (serum ferritin (SF) <14pmol/L and TS <10%) or iron depletion (SF<112pmol/L). We performed direct sequencing of TMPRSS6 exons 7 and 17 in each patient. We used age, TS, SF, Hb, MCV, pica, and TMPRSS6 allele positivity (dichotomous) or mutation genotypes (trichotomous) as variables for analyses. RESULTS: Forty-six women were white; two were black. 58.3% had iron deficiency. 45.8% had pica (pagophagia, each case). Allele frequencies were 41.7% (K253E), 36.5% (A736V), and 39.6% (Y739Y). K253E frequency was greater in women with TS ≥10% (p=0.0001). Y739Y was more frequent in women with TS <10% (p=0.0135). Mean TS was also lower in women positive for Y739Y (6±4% vs. 13±16%, respectively; p=0.0021). In multiple regressions, neither K253E, A736V, nor Y739Y genotypes were significantly associated with other variables. CONCLUSIONS: TMPRSS6 K253E frequency was greater in women with TS ≥10%. Frequency of Y739 was greater in women with TS <10%. Mean TS was lower in women with Y739Y. We observed no other significant relationship of TMPRSS6 K253E, A736V, or Y739Y with iron, erythrocyte, or pica phenotypes.

Mild iron overload in an African American man with SLC40A1 D270V.

We report on a 46-year-old black man who resided in Alabama with normal transferrin saturation, mild hyperferritinemia, chronic hepatitis C, and 3+ iron in hepatocytes and Kupffer cells. Exome sequencing revealed heterozygosity for SLC40A1 D270V (exon 7, c.809A→T), a mutation previously reported only in 1 black patient with iron overload who resided in the Republic of South Africa. The present patient was also heterozygous for: heme transporter FLVCR1 novel allele P542S (exon 10, 1624C→T); FLVCR1 T544M (rs3207090); hemopexin (HPX) R371W (rs75307540); ferritin scavenger receptor (SCARA5) R471H (rs61737287); and transferrin receptor (TFRC) G420S (rs41295879). He had no HFE, TFR2,HJV, or HAMP mutations. D270V was not detected in 19 other African Americans with iron overload who resided in Alabama. The allele frequency of SLC40A1 D270V in 258 African American adults who participated in a health appraisal clinic was 0.0019 (95% confidence interval 0-0.0057). D270V could explain 'classical' ferroportin hemochromatosis phenotypes in some African Americans.

Multi-organ iron overload in an African-American man with ALAS2 R452S and SLC40A1 R561G.

BACKGROUND: X-linked sideroblastic anemia (XLSA) is associated with iron overload and mutations in ALAS2, which encodes 5-aminolevulinate synthase. There are few reports of XLSA in persons of sub-Saharan African descent. METHODS: A 47-year-old African-American man had microcytic anemia, elevated iron measures, cardiomyopathy, hepatic cirrhosis, diabetes mellitus, a history of cocaine use and hepatitis C. We amplified and directly sequenced his genomic DNA to detect mutations of SLC40A1, HFE, TFR2, HAMP, HJV and ALAS2. RESULTS: The subject's transferrin saturation was 100% and his serum ferritin was 2,960 ng/ml. An MRI scan revealed diffusely decreased T(2) signals of the heart, liver and pancreas. Transjugular right endomyocardial and liver biopsy specimens revealed marked iron deposition in cardiac myocytes and hepatocytes, and cirrhosis. He died of progressive cardiomyopathy. He was hemizygous for ALAS2 R452S (exon 9; c.1354C-->A) and heterozygous for SLC40A1 R561G (exon 8; c.1681A-->G). He did not have coding region mutations in HFE, TFR2, HAMP or HJV. CONCLUSIONS: ALAS2 R452S largely explains this patient's microcytic anemia and multi-organ iron overload and dysfunction. SLC40A1 R561G may have increased his iron absorption and overload further. Acquired factors, especially cocaine use and hepatitis C, may have contributed to his clinical phenotype.

SLC40A1 c.1402G-->a results in aberrant splicing, ferroportin truncation after glycine 330, and an autosomal dominant hemochromatosis phenotype.

BACKGROUND/AIMS: To determine the molecular basis of a mild hemochromatosis phenotype in a man of Scottish-Irish descent. METHODS: We sequenced genomic DNA to detect mutations of HFE, SLC40A1, TFR2, HAMP, and HFE2. RNA isolated from blood mononuclear cells was used to make cDNA. RT-PCR was performed to amplify ferroportin from cDNA, and amplified products were visualized by electrophoresis and sequenced. RESULTS: The proband was heterozygous for the novel mutation c.1402G-->A (predicted G468S) in exon 7 of the ferroportin gene (SLC40A1). Located in the last nucleotide before the splice junction, this mutation results in aberrant splicing to a cryptic upstream splice site located at nt 990 within the same exon. This causes truncation of ferroportin after glycine 330 and the addition of 4 irrelevant amino acids before terminating. The truncated ferroportin protein, missing its C-terminal 241 amino acids, would lack all structural motifs beyond transmembrane region 7. The patient was also heterozygous for the common HFE H63D polymorphism, but did not have coding region mutations in TFR2, HAMP, or HFE2. CONCLUSIONS: We conclude that this patient represents a unique example of hemochromatosis due to a single base-pair mutation of SLC40A1 that results in aberrant splicing and truncation of ferroportin.

Intravenous Bevacizumab Therapy in a Patient with Hereditary Hemorrhagic Telangiectasia, ENG E137K, Alcoholic Cirrhosis, and Portal Hypertension.

Intravenous bevacizumab decreased mucosal bleeding in some patients with hereditary hemorrhagic telangiectasia (HHT). We treated a 47-year-old male who had HHT, severe epistaxis, and gastrointestinal bleeding, alcoholic cirrhosis, and portal hypertension with intravenous bevacizumab 2.5 mg/kg every 2 weeks. We tabulated these measures weekly during weeks 1-33 (no bevacizumab); 34-57 (bevacizumab); and 58-97 (no bevacizumab): hemoglobin (Hb) levels; platelet counts; units of transfused packed erythrocytes (PRBC units); and quantities of iron infused as iron dextran to support erythropoiesis. We performed univariate and multivariable analyses. We sequenced his ENG and ACVRL1 genes. Epistaxis and melena decreased markedly during bevacizumab treatment. He reported no adverse effects due to bevacizumab. Mean weekly Hb levels were significantly higher and mean weekly PRBC units and quantities of intravenous iron were significantly lower during bevacizumab treatment. We performed a multiple regression on weekly Hb levels using these independent variables: bevacizumab treatment (dichotomous); weekly platelet counts; weekly PRBC units; and weekly quantities of intravenous iron. There was 1 positive association: (bevacizumab treatment; p = 0.0046) and 1 negative association (PRBC units; p = 0.0004). This patient had the novel ENG mutation E137K (exon 4; c.409G→A). Intravenous bevacizumab treatment 2.5 mg/kg every 2 weeks for 24 weeks was well-tolerated by a patient with HHT due to ENG E137K and was associated with higher weekly Hb levels and fewer weekly PRBC units.

Genetic polymorphisms and susceptibility to lung disease.

Susceptibility to infection by bacterium such as Bacillus anthracis has a genetic basis in mice and may also have a genetic basis in humans. In the limited human cases of inhalation anthrax, studies suggest that not all individuals exposed to anthrax spores were infected, but rather, individuals with underlying lung disease, particularly asthma, sarcoidosis and tuberculosis, might be more susceptible. In this study, we determined if polymorphisms in genes important in innate immunity are associated with increased susceptibility to infectious and non-infectious lung diseases, particularly tuberculosis and sarcoidosis, respectively, and therefore might be a risk factor for inhalation anthrax. Examination of 45 non-synonymous polymorphisms in ten genes: p47phox (NCF1), p67phox (NCF2), p40phox (NCF4), p22phox (CYBA), gp91phox (CYBB), DUOX1, DUOX2, TLR2, TLR9 and alpha 1-antitrypsin (AAT) in a cohort of 95 lung disease individuals and 95 control individuals did not show an association of these polymorphisms with increased susceptibility to lung disease.

Regulation of hepcidin and iron-overload disease.

Hepcidin, a 25-amino-acid antimicrobial peptide, is the central regulator of iron homeostasis. Hepcidin transcription is upregulated by inflammatory cytokines, iron, and bone morphogenetic proteins and is downregulated by iron deficiency, ineffective erythropoiesis, and hypoxia. The iron transporter ferroportin is the cognate receptor of hepcidin and is destroyed as a result of interaction with the peptide. Except for inherited defects of ferroportin and hepcidin itself, all forms of iron-storage disease appear to arise from hepcidin dysregulation. Studies using multiple approaches have begun to delineate the molecular mechanisms that regulate hepcidin expression, particularly at the transcriptional level. Knowledge of the regulation of hepcidin by inflammation, iron, erythropoiesis, and hypoxia will lead to an understanding of the pathogenesis of primary hemochromatosis, secondary iron overload, and anemia of inflammatory disease.

SLC40A1 Q248H allele frequencies and Q248H-associated risk of non-HFE iron overload in persons of sub-Saharan African descent.

The ferroportin polymorphism SLC40A1 Q248H (exon 6, cDNA 744G-->T; Gln248His) occurs in persons of sub-Saharan African descent with and without iron overload, and is associated with elevated serum ferritin concentrations (SF). However, the risk of iron overload associated with Q248H has not been defined. We tabulated previously reported Q248H allele frequency estimates in African-Americans and Native Africans, and computed the risk of iron overload associated with Q248H in subjects who lacked HFE C282Y. The aggregate Q248H allele frequency in 1038 African-Americans in two cohorts from Alabama and one cohort each from Washington, DC and California was 0.0525 (95% CI: 0.0451, 0.0652); there was no significant difference in frequencies across these cohorts. The aggregate frequency in 259 Natives from southeast Africa in two cohorts was 0.0946 (95% CI: 0.0694, 0.1198); the difference between the frequencies of these cohorts was not significant. The aggregate Q248H frequencies in African-Americans and Native Africans differed significantly (0.0525 vs. 0.0946, respectively; p=0.0021). There were reports of 24 unrelated African-Americans and 15 unrelated Native Africans without HFE C282Y who had iron overload. In African-Americans, the odds ratio (OR) of Q248H-associated risk of iron overload using 610 C282Y-negative control subjects unselected for SF was 1.57 (95% CI: 0.52, 4.72; p=0.29). In Native Africans, the OR using 208 control subjects unselected for SF was 1.05 (95% CI: 0.28, 3.90; p=0.58). We conclude that the frequency of SLC40A1 Q248H is significantly lower in African-Americans than in Native Africans. Although OR estimates of iron overload in African-Americans and Native Africans with Q248H were greater than unity, the increased OR were not statistically significant.

Hemochromatosis and severe iron overload associated with compound heterozygosity for TFR2 R455Q and two novel mutations TFR2 R396X and G792R.

We report three mutations of transferrin receptor 2 (TFR2)--R396X (exon 9; nt 1186C-->T), R455Q (exon 10; nt 1364G-->A) and G792R (exon 18; nt 2374G-->A)--in a man of Scottish descent with hemochromatosis and severe iron overload. He was also heterozygous for the common HFE H63D polymorphism. The patient did not have coding region mutations in HAMP, FPN1, HJV or ALAS2. We conclude that this patient represents another example of hemochromatosis due to mutations of the gene encoding transferrin receptor 2.

Disparate phenotypic expression of ALAS2 R452H (nt 1407 G --> A) in two brothers, one with severe sideroblastic anemia and iron overload, hepatic cirrhosis, and hepatocellular carcinoma.

We report the case of a man with severe X-linked sideroblastic anemia, severe iron overload, and hepatic cirrhosis who died of hepatocellular carcinoma. Evaluation of family members using DNA sequencing revealed that he was hemizygous for the novel ALAS2 mutation R452H (exon 9; nt 1407 G --> A). The proband's brother, an ALAS2 R452H hemizygote, had mild anemia and mild iron overload. Four female relatives were ALAS2 R452H heterozygotes, but they had mild or no anemia and no iron overload. Sequencing of TFR2, HFE, FPN1 (SLC40A1), HAMP, HJV, and the erythrocyte pyruvate kinase genes of family members was also performed. We thus detected the novel TFR2 missense mutation I449V (exon 10; nt 1345 A --> G) in the proband's wife and daughter, neither of whom had anemia or iron overload. Possible explanations for the disparate red blood cell and iron phenotypes of the proband and his family members are discussed.

Iron overload and prolonged ingestion of iron supplements: clinical features and mutation analysis of hemochromatosis-associated genes in four cases.

We evaluated and treated four white adults (one man, three women) who had iron overload associated with daily ingestion of iron supplements for 7, 15, 35, and 61 years, respectively. We performed HFE mutation analysis to detect C282Y, H63D, and S65C in each patient; in two patients, HFE exons were sequenced. In two patients, direct sequencing was performed to detect coding region mutations of TFR2, HAMP, FPN1, HJV, and ALAS2. Patients 1-4 ingested 153, 547, 1,341, and 4,898 g of inorganic iron as supplements. Patient 1 had hemochromatosis, HFE C282Y homozygosity, and beta-thalassemia minor. Patient 2 had spherocytosis and no HFE coding region mutations. Patient 3 had no anemia, a normal HFE genotype, and no coding region mutations in HAMP, FPN1, HJV, or ALAS2; she was heterozygous for the TFR2 coding region mutation V583I (nt 1,747 G-->A, exon 15). Patient 4 had no anemia and no coding region mutations in HFE, TFR2, HAMP, FPN1, HJV, or ALAS2. Iron removed by phlebotomy was 32.4, 10.4, 15.2, and 4.0 g, respectively. There was a positive correlation of log(10) serum ferritin and the quantity of iron removed by phlebotomy (P = 0.0371). Estimated absorption of iron from supplements in patients 1-4 was 20.9%, 1.9%, 1.1%, and 0.08%. We conclude that the clinical phenotypes and hemochromatosis genotypes of adults who develop iron overload after ingesting iron supplements over long periods are heterogeneous. Therapeutic phlebotomy is feasible and effective, and would prevent complications of iron overload.

Three kinships with ALAS2 P520L (c. 1559 C --> T) mutation, two in association with severe iron overload, and one with sideroblastic anemia and severe iron overload.

Mutations in aminolevulinate synthase 2 (ALAS2) are usually associated with sideroblastic anemia and iron overload. The objective of this study was to determine if "mild" mutations in ALAS2 might increase the severity of primary iron overload. Direct sequencing of the ALAS2 gene was performed on 24 subjects with primary hemochromatosis and one subject with sideroblastic anemia with severe iron overload. We identified a novel mutation P520L (c. 1559 C --> T) in ALAS2 in three subjects. Two had severe iron overload and no anemia: one also had HFE C282Y homozygosity, and the other was wildtype for HFE and other iron-related genes. The third subject had sideroblastic anemia with iron overload, and was hemizygous for both P520L and R560H (c. 1679 G --> A) mutations in ALAS2. The P520L mutation was found at a frequency of 0.0013 (741 alleles) in white control subjects, but was not found in 158 alleles from black control subjects. The proline in this position is highly conserved across species from humans to zebrafish. However, genotype/phenotype studies of the families demonstrate that the P520L mutation alone has no iron-associated phenotype, but it may act as a modifier of iron overload in the presence of mutations in HFE or other uncharacterized hemochromatosis genes. Thus, ALAS2 mutations might contribute to more severe iron loading in persons with primary hemochromatosis.

Iron overload in an African American woman with SS hemoglobinopathy and a promoter mutation in the X-linked erythroid-specific 5-aminolevulinate synthase (ALAS2) gene.

We report the case of an African American woman with sickle cell anemia and iron overload incompletely explained by erythrocyte transfusion who is heterozygous for a promoter mutation in the X-linked erythroid-specific 5-aminolevulinate synthase gene (ALAS2): a C to G transversion at nucleotide -206 from the transcription start site, as defined by primer extension (-258 from the start ATG). This mutation has previously been associated with sideroblastic anemia and iron overload in members of a Welsh kinship. No coding region mutation of HFE, FPN1, TFR2, HAMP, or HJV genes was detected. The mother of the proband has mild, chronic anemia and is also heterozygous for the same proximal promoter region mutation of ALAS2. However, she has no evidence of iron overload. We conclude that an ALAS2 promoter region mutation could partly account for iron overload in the present proband, and that this or other ALAS2 mutations could explain the occurrence of iron overload in other whites or blacks with or without anemia. The occurrence of anemia and iron overload may be discordant in women heterozygous for ALAS2 mutations.

The mitochondrial nt 16189 polymorphism and hereditary hemochromatosis.

It has been claimed that a noncoding mitochondrial polymorphism at nt 16189 is correlated with the penetrance of the homozygous state for the C282Y mutation of the HFE gene. We have genotyped homozygotes for the C282Y mutation and find no relationship between the ferritin levels and the inheritance of the mitochondrial polymorphism. Indeed, the small difference found is in the opposite direction of that reported previously.

Genetic abnormalities and juvenile hemochromatosis: mutations of the HJV gene encoding hemojuvelin.

Juvenile hemochromatosis is an early-onset form of iron storage disease characterized by hypogonadotrophic hypogonadism and cardiomyopathy. Recently, the putative causative gene (LOC148738) encoding a protein designated hemojuvelin was cloned. The previously proposed designation of this gene as HFE2 is contrary to established convention, because it is not a member of the HFE family. We suggest that it be designated HJV. We sequenced this gene in members of 2 previously reported kinships that manifest typical juvenile hemochromatosis. In one kinship, 2 previously undescribed mutations of HJV were identified, c.238T>C (C80R) and c.302T>C (L101P). In the second kinship, 2 previously identified mutations, G320V and I222N, were found. These studies confirm that mutations in HJV cause juvenile hemochromatosis.

Hemojuvelin (HJV) mutations in persons of European, African-American and Asian ancestry with adult onset haemochromatosis.

Mutations in the chromosome 1q-linked gene hemojuvelin (HJV) have recently been found to be a cause of juvenile haemochromatosis. We addressed the question of whether hemojuvelin mutations may influence the phenotype of patients with adult-onset haemochromatosis with or without mutations of the HFE gene. We sequenced the complete coding region of 133 subjects with iron overload. To screen a large number of patients, we also developed conditions for analysis by denaturing high-performance liquid chromatography (dHPLC). This diagnostic modality detects many mutations of the HJV gene. One patient with severe iron overload was found to be a compound heterozygote for HJV mutations, one of which had previously been identified in patients with juvenile haemochromatosis (G320V) and the other was novel (C321W). A number of other mutations were identified, but none were clearly associated with increases in the body iron burden. Notable among these was a DNA triplet insert, predicting an insertion of glycine, found in two African-American subjects, one with and one without iron storage disease.

Polymorphisms in iron-responsive binding protein 2 and lack of association with sporadic Parkinson's disease.

Mice with targeted disruptions in the iron-responsive binding protein 2 (IRP2) gene accumulate iron in distinct regions of the brain and develop neurodegenerative characteristics resembling Parkinson's disease after 6 months of age. To determine whether polymorphisms in IRP2 predispose humans to Parkinson's disease (PD), we sequenced the IRP2 gene of subjects with sporadic PD and normal controls. Three polymorphisms which result in an amino acid change were identified: L159V, F272L, and T560I. The L159V and T560I polymorphisms, identified in an African-American PD subject, were found in the African-American population at an allele frequency of 0.102 (n = 1,236) and 0.111 (n = 1,228), respectively, and were not associated with an increased prevalence of PD. The F272L polymorphism was found in a normal 58-year-old, Caucasian subject whose father had PD, but it was not observed in 38 additional patients with sporadic PD. The F272L polymorphism occurred at an allele frequency of 0.0014 (n = 1,384) in the normal Caucasian population. Additional F272L heterozygous subjects identified in the normal population did not have a family or personal history of PD. We conclude that these IRP2 polymorphisms do not play an important role in the development of sporadic cases of PD. It remains to be determined whether other polymorphisms in IRP2 play a role in familial PD.

Ferroportin 1 (SCL40A1) variant associated with iron overload in African-Americans.

We find that in the Black American population average ferritin levels are higher than those in Whites, both among men and women. African-Americans have an increased prevalence of iron storage disease characterized by prominent iron deposition in macrophages of the liver and other organs. The iron distribution in patients with mutations of the ferroportin gene is similar. A c.744 G-->T (Gln 248 His) mutation was detected among African-Americans at polymorphic frequencies. This variant is associated with increased ferritin levels in African-Americans and may play a role in their propensity to develop iron overload.