Differences in the frequency of genetic variants associated with iron imbalance among global populations

Genetic and neuro-epigenetic effects of divergent artificial selection for feather pecking behaviour in chickens

Feather pecking (FP) is a repetitive behaviour in chickens, influenced by genetic, epigenetic, and environmental factors, similar to behaviours seen in human developmental disorders (e.g., hyperactivity, autism). This study examines genetic and neuro-epigenetic factors in the thalamus of chickens from lines selected for seven generations for high or low FP behaviour (HFP or LFP). We integrate data on Differentially Methylated Regions (DMRs), Single Nucleotide Polymorphisms (SNPs), and Copy Number Variations (CNVs) in this controlled artificial selection process. Significant differences in behaviour, immunology, and neurology have been reported in these lines. We identified 710 SNPs in these lines that indicate new potentially important genes for FP such as TMPRSS6 (implicated in autism), and SST and ARNT2 (somatostatin function). CNV were the omic level most affected during selection. The largest CNVs found were in RIC3 (gain in HFP) and SH3RF2 (gain in LFP) genes, linked to nicotinic acetylcholine receptor regulation and human oncogenesis, respectively. Our study also suggests that promoters and introns are hotspots for CpG depletion. The overlapping of the omic levels investigated here with data from a public FP Quantitative Trait Loci (QTL) database revealed novel candidate genes for understanding repetitive behaviours, such as RTKN2, associated with Alzheimer's disease in humans. This study suggests CNVs as a crucial initial step for genomic diversification, potentially more impactful than SNPs.

The association of TMPRSS6 gene polymorphism with iron status in Egyptian children (a pilot study)

Several studies have shown association of single nucleotide polymorphisms (SNPs) of hepcidin regulatory pathways genes with impaired iron status. The most common is in the TMPRSS6 gene. In Africa, very few studies have been reported. We aimed to investigate the correlation between the common SNPs in the transmembrane protease, serine 6 (TMPRSS6) gene and iron indicators in a sample of Egyptian children for identifying the suitable candidate for iron supplementation.Patients and methods One hundred and sixty children aged 5-13 years were included & classified into iron deficient, iron deficient anemia and normal healthy controls. All were subjected to assessment of serum iron, serum ferritin, total iron binding capacity, complete blood count, reticulocyte count, serum soluble transferrin receptor and serum hepcidin. Molecular study of TMPRSS6 genotyping polymorphisms (rs4820268, rs855791 and rs11704654) were also evaluated.Results There was an association of iron deficiency with AG of rs855791 SNP, (P = 0.01). The minor allele frequency for included children were 0.43, 0.45 & 0.17 for rs4820268, rs855791 & rs11704654 respectively. Genotype GG of rs4820268 expressed the highest hepcidin gene expression fold, the lowest serum ferroportin & iron store compared to AA and AG genotypes (p = 0.05, p = 0.05, p = 0.03 respectively). GG of rs855791 had lower serum ferritin than AA (p = 0.04), lowest iron store & highest serum hepcidin compared to AA and AG genotypes (p = 0.04, p = 0.01 respectively). Children having CC of rs11704654 had lower level of hemoglobin, serum ferritin and serum hepcidin compared with CT genotype (p = 0.01, p = 0.01, p = 0.02) respectively.Conclusion Possible contribution of SNPs (rs855791, rs4820268 and rs11704654) to low iron status.

High CDT without clinical context: beware of the variant

Carbohydrate-deficient transferrin (CDT) is a performant biomarker used for the diagnosis of chronic alcohol abuse. Here, we describe the case of a 39-year-old male of Tamil ethnicity who had extremely elevated (20%) CDT using capillary electrophoresis (but without glycoforms profile analysis), putting his driving license regranting at risk. However, the patient had no symptoms of chronic alcohol abuse, normal mean corpuscular volume and gamma-glutamyl transferase, and did not admit to any alcohol consumption. Re-analysis by N-Latex CDT immunoassay revealed a CDT at 1.7%. Further investigation by whole-exome sequencing revealed a c.1295A>G missense variant at the heterozygous state on the TFgene. This variant is characterized by an amino-acid change at a consensus sequence forN-glycosylation. Therefore, half of the patient transferrin proteins were lacking a completeN-glycan chain out of two, despite no alcohol consumption. This also explains the discrepancies between the techniques, as the N-Latex antibodies did not recognize the mutated sequence. In conclusion, this case highlights the importance of comparing laboratory results between themselves and the clinical description, the absolute requirement for glycoforms profile analysis before delivering results, and the necessity to confirm intriguing results by another technique in a specialized laboratory.

Gene polymorphisms within regions of complement component C1q in HIV associated preeclampsia

OBJECTIVE

This study investigates the association of C1q gene (rs292001 and rs294183) polymorphisms in HIV infected and uninfected preeclamptic women of African ancestry.

MATERIALS AND METHODS

The study population consisted of 325 pregnant women of African ancestry grouped into 145 normotensive pregnant women (72 HIV uninfected normotensive, 73 HIV infected normotensive) and 180 preeclamptic pregnant women (103 HIV uninfected preeclamptics, 77 HIV infected preeclamptics). Preeclamptic pregnant women were further sub-grouped into 79 early-onset preeclampsia (EOPE) (40 HIV uninfected EOPE, 39 HIV infected EOPE) and 101 late-onset preeclampsia (LOPE) (63 HIV uninfected LOPE, 38 HIV infected LOPE). Genotyping of complement C1q gene polymorphisms (rs292001 and rs294183) was detected using a TaqMan® SNP Genotyping assay from purified DNA.

RESULTS

No significant differences in allelic and genotype frequencies of rs292001 and rs294183 between preeclamptic and normotensive women were observed. Likewise, there were no significant differences in allelic and genotype frequencies between HIV infected normotensive vs HIV infected preeclampsia and HIV uninfected normotensive vs HIV uninfected preeclampsia for both SNPs. However, the odds ratio of preeclamptic women having the GA genotype was 1:2.

CONCLUSION

We demonstrate that SNPs of the C1q gene (rs292001 and rs294183) are not associated with the pathogenesis of PE development in women of African ancestry. The role ofC1qrs292001 heterozygous GA is highlighted (with and without HIV infection) may affect susceptibility to PE development. Notably, this dysregulation may affect C1q translation and protein output thus influencing the downstream role of the complement system and functional immunology in HIV infection comorbid with PE.

TMPRSS6 rs855791 polymorphism is associated with iron deficiency in a cohort of Sri Lankan pregnant women

Background

Hepcidin is the key regulator of systemic iron homeostasis and is downregulated by matriptase 2 (MT2), a protease encoded by TMPRSS6 gene. In the presence of low iron levels, MT2 cleaves membrane-bound hemojuvelin (HJV), causing a negative regulation of hepcidin at the gene level, and restores iron balance. rs855791T > C, a missense variant in the catalytic domain of MT2, causes valine to alanine change at 736 position. The current study aimed to investigate the association of TMPRSS6 rs855791 on iron status among a cohort of pregnant women in Sri Lanka and to predict the possible molecular mechanisms.

Methods

The study was conducted among 73 pregnant women at ≤ 12 weeks of gestation. Iron deficiency was defined as serum ferritin < 30 μg/L after adjusting for inflammation. rs855791 was genotyped with a PCR–RFLP, and its association with iron deficiency was analyzed using binary logistic regression. Docking of HJV with MT2 protein encoded by the two rs855791 alleles was undertaken in silico to predict the molecular mechanism of the observed associations.

Results

The majority of the study population (70%) were iron deficient. Among the subjects, T allele was prevalent in the iron deficient group with a frequency of 61.8%, with a nearly twofold enhanced risk for iron deficiency (OR = 2.566, 95%CI; P = 0.011). For TT genotype, the risk of iron deficiency was nearly sixfold (OR = 5.867; 95%CI; P = 0.023). According to the in silico analysis, MT2 736A and HJV complex is more stable with an interface energy of − 7.934 kJ/mol compared to the MT2 736 V and HJV complex which generates an interface energy of − 4.689 kJ/mol.

Conclusion

The current study suggests that the iron regulatory effect of rs855791 of TMPRSS6 is brought about by the differences in thermodynamic stability of the two protein complexes made by MT2 and HJV proteins. The prevalence of iron deficiency observed among Sri Lankan pregnant women may be an interplay between the prevalence of rs855791 T allele and the low dietary iron intake.

Genetic Aspects of Micronutrients Important for Inflammatory Bowel Disease

Inflammatory bowel disease (IBD), Crohn’s disease (CD) and ulcerative colitis (UC) are complex diseases whose etiology is associated with genetic and environmental risk factors, among which are diet and gut microbiota. To date, IBD is an incurable disease and the main goal of its treatment is to reduce symptoms, prevent complications, and improve nutritional status and the quality of life. Patients with IBD usually suffer from nutritional deficiency with imbalances of specific micronutrient levels that contribute to the further deterioration of the disease. Therefore, along with medications usually used for IBD treatment, therapeutic strategies also include the supplementation of micronutrients such as vitamin D, folic acid, iron, and zinc. Micronutrient supplementation tailored according to individual needs could help patients to maintain overall health, avoid the triggering of symptoms, and support remission. The identification of individuals’ genotypes associated with the absorption, transport and metabolism of micronutrients can modify future clinical practice in IBD and enable individualized treatment. This review discusses the personalized approach with respect to genetics related to micronutrients commonly used in inflammatory bowel disease treatment.

Common Single Nucleotide Polymorphism of TMPRSS6, an Iron Regulation Gene, Associated with Variable Red Blood Cell Indices in Deletional α-Globin Genotypes

Red blood cell (RBC) indices, including mean corpuscular volume (MCV) and mean corpuscular haemoglobin (MCH), have been widely used for primary screening for thalassaemia (thal) syndromes. Recently, a single nucleotide polymorphism (SNP) rs855791 of TMPRSS6, an iron regulation gene involved in the substitution of a nucleotide between thymine (T) and cytosine (C) in exon 17 resulted in an amino acid change, p.Val736Ala (V736A), has been described to associate with RBC indices. The objective was to study the effects of common SNP V736A on RBC indices in deletional α-thal variations. SNP rs855791 genotypes were identified from 433 Thai volunteers, including 32.6% males and 67.4% females with an average age of 23.0 ± 8.7 years. These populations included individuals (82.4%) who had normal globin genotype (αα/αα, ββ) and α-thal carriers, which were divided into two subgroups, including α⁺-thal (-α/αα) (14.1%) and α^o-thal (--/αα) (3.5%). Among three SNP genotypes, the C allele gradually expressed higher MCV and MCH than those of the T allele in both α⁺- and α^o-thal traits. Importantly, SNP rs855791 of TMPRSS6 responded to α-globin deletions for sustaining RBC sizes and haemoglobinisation in α-thal carriers.

Ethnic differences in adverse iron status in early pregnancy: a cross-sectional population-based study

We studied ethnic differences in terms of iron status during pregnancy between Dutch women and other ethnicities and explore to what extent these differences can be explained by environmental factors. This cross-sectional population-based study (2002-2006) was embedded in the Generation R study and included a total of 4737 pregnant women from seven ethnic groups (Dutch, Turkish, Moroccan, Cape Verdean, Surinamese-Hindustani, Surinamese-Creole and Antillean). Ethnicity was defined according to the Dutch classification of ethnic background. Ferritin, iron and transferrin were measured in early pregnancy. The overall prevalence of iron deficiency was 7 %, ranging from 4 % in both Dutch and Surinamese-Creoles, to 18 % in Turkish, Moroccan and Surinamese-Hindustani women. Iron overload was most prevalent in Surinamese-Creole (11 %) and Dutch (9 %) women. Socioeconomic factors accounted for 5-36 % of the differences. Income was the strongest socioeconomic factor in the Cape Verdean and Surinamese-Hindustani groups and parity for the Turkish and Moroccan groups. Lifestyle determinants accounted for 8-14 % of the differences. In all groups, the strongest lifestyle factor was folic acid use, being associated with higher iron status. In conclusion, in our population, both iron deficiency and iron overload were common in early pregnancy. Our data suggest that ethnic differences in terms of socioeconomic and lifestyle factors only partly drive the large ethnic differences in iron status. Our data support the development of more specific prevention programmes based on further exploration of socioeconomic inequities, modifiable risk and genetic factors in specific ethnic subgroups, as well as the need for individual screening of iron status before supplementation.

Estimates of West African Ancestry in African Americans Using Alleles of Iron-Related Genes HJV, SLC40A1, and TFR2

Background: Few studies have estimated African ancestry of African Americans (AA). In sub-Saharan West African (WA) Blacks, some nonancestral alleles of iron-related genes HJV, SLC40A1, and TFR2 are common, whereas in European Americans (EA) the same alleles are rare. These alleles have not been used to estimate WA Black ancestry in AA. Methods: We estimated WA Black ancestry in AA (M) using published HJV c.929C>G (rs7540883), SLC40A1 c.744G>T (rs11568350), and TFR2 c.713C>T (rs34242818) allele frequencies in WA Blacks, AA, and EA. We computed standard error (SE) and one-sided 95% confidence intervals (CI) for each M. Results: The combined representation of WA Blacks from The Gambia and Nigeria was 79-89%. Aggregate HJV, SLC40A1, and TFR2 allele frequencies in WA Blacks were 0.1025 [95% CI: 0.0835-0.1253] (n = 405), 0.0517 [0.0469-0.0569] (n = 3839), and 0.1432 [0.1202-0.1697] (n = 405), respectively. Aggregate HJV, SLC40A1, and TFR2 allele frequencies in AA were 0.0718 [0.0648-0.0797] (n = 2352), 0.0557 [0.0506-0.0613] (n = 3590), and 0.1224 [0.1132-0.1322] (n = 2352), respectively. Aggregate HJV, SLC40A1, and TFR2 allele frequencies in 4449 EA were 0.0002 [0-0.0009], 0.0003 [0.0001-0.0010], and 0.0004 [0.0001-0.0012], respectively. M (SE [one-sided 95% CI]) for HJV, SLC40A1, and TFR2 alleles was 0.7006 (0.0818 [0.5402-1.0000]), 1.0000 (0.0752 [0.9306-1.0000]), and 0.8546 (0.0810 [0.6959-1.0000]), respectively. Mean of these M is 0.8777 (87.8%). Conclusions: The mean proportional WA Black ancestry in AA of 87.8% using HJV c.929C>G, SLC40A1 c.744G>T, and TFR2 c.713C>T allele frequencies is consistent with that of previous studies that used other autosomal markers and methods.

Iron homeostasis and organismal aging

Iron is indispensable for normal body functions across species because of its critical roles in red blood cell function and many essential proteins and enzymes required for numerous physiological processes. Regulation of iron homeostasis is an intricate process involving multiple modulators at the systemic, cellular, and molecular levels. Interestingly, emerging evidence has demonstrated that many modulators of iron homeostasis contribute to organismal aging and longevity. On the other hand, the age-related dysregulation of iron homeostasis is often associated with multiple age-related pathologies including bone resorption and neurodegenerative diseases such as Alzheimer's disease. Thus, a thorough understanding on the interconnections between systemic and cellular iron balance and organismal aging may help decipher the etiologies of multiple age-related diseases, which could ultimately lead to developing therapeutic strategies to delay aging and treat various age-related diseases. Here we present the current understanding on the mechanisms of iron homeostasis. We also discuss the impacts of aging on iron homeostatic processes and how dysregulated iron metabolism may affect aging and organismal longevity.

Dietary iron to total energy intake ratio and type 2 diabetes incidence in a longitudinal 12-year analysis of the Korean Genome and Epidemiology Cohort Study

PURPOSE

Recent study found iron consumption has been associated with an increased risk of type 2 diabetes (T2DM). Even though, high iron intake is correlated with total caloric intake, most studies have evaluated the individual effect of iron and total caloric intake. The aim of this study was to investigate the effect of iron intake, in conjunction with total energy intake, on developing T2DM. We also investigated the interactions between dietary iron and energy ratios (IERs) and iron-related single nucleotide polymorphisms (SNPs) in the development of T2DM.

METHODS

The study was carried out in Ansan and Ansung, Korea, between March 2001 and December 2014. A total of 6413 participants (3073 men and 3340 women), aged 40-69 years, were enrolled in this study. The mean follow-up period was 8.4 years. The study population was divided into quartiles based on IERs with cut-off points at 4.54, 5.41, and 6.29. The odds ratios (ORs) for new-onset T2DM were calculated across each quartile of IERs and a random forest model was constructed using the default settings to predict new-onset T2DM. To confirm the interaction among IERs, SNPs, and the incidence of T2DM, we measured the predictive power of new-onset T2DM using IER and six SNPs in genes related to iron metabolism [rs855791 (TPMRSS6), rs38116479 (TF), rs1799852 (TF), rs2280673, rs1799945 (HFT), rs180562 (HFE)].

RESULTS

The prevalence of T2DM was 762 (11.8%). IERs showed a positive association with T2DM. The ORs were 1.30 (95% CI 1.02-1.67), 1.20 (95% CI 0.94-1.56), and 1.43 (95% CI 1.11-1.86) across the IER quartiles after adjusting for non-dietary and dietary metabolic risk factors. When the IER was 1.89-fold higher than the reference group, the risk of developing T2DM increased by 43% (OR 1.43; 95% CI 1.11-1.86).

CONCLUSION

A higher IER was positively associated with developing T2DM independent of dietary or non-dietary risk factors. We also found the possible interactions between the identified SNPs and iron intake in relations to T2DM.

Ethnic Differences in Iron Status

Iron is unique among all minerals in that humans have no regulatable excretory pathway to eliminate excess iron after it is absorbed. Iron deficiency anemia occurs when absorbed iron is not sufficient to meet body iron demands, whereas iron overload and subsequent deposition of iron in key organs occur when absorbed iron exceeds body iron demands. Over time, iron accumulation in the body can increase risk of chronic diseases, including cirrhosis, diabetes, and heart failure. To date, only ∼30% of the interindividual variability in iron absorption can be captured by iron status biomarkers or iron regulatory hormones. Much of the regulation of iron absorption may be under genetic control, but these pathways have yet to be fully elucidated. Genome-wide and candidate gene association studies have identified several genetic variants that are associated with variations in iron status, but the majority of these data were generated in European populations. The purpose of this review is to summarize genetic variants that have been associated with alterations in iron status and to highlight the influence of ethnicity on the risk of iron deficiency or overload. Using extant data in the literature, linear mixed-effects models were constructed to explore ethnic differences in iron status biomarkers. This approach found that East Asians had significantly higher concentrations of iron status indicators (serum ferritin, transferrin saturation, and hemoglobin) than Europeans, African Americans, or South Asians. African Americans exhibited significantly lower hemoglobin concentrations compared with other ethnic groups. Further studies of the genetic basis for ethnic differences in iron metabolism and on how it affects disease susceptibility among different ethnic groups are needed to inform population-specific recommendations and personalized nutrition interventions for iron-related disorders.

Association of common TMPRSS6 and TF gene variants with hepcidin and iron status in healthy rural Gambians

Genome-wide association studies in Europeans and Asians have identified numerous variants in the transmembrane protease serine 6 (TMPRSS6) and transferrin (TF) genes that are associated with changes in iron status. We sought to investigate the effects of common TMPRSS6 and TF gene SNPs on iron status indicators in a cohort of healthy Africans from rural Gambia. We measured iron biomarkers and haematology traits on individuals participating in the Keneba Biobank with genotype data on TMPRSS6 (rs2235321, rs855791, rs4820268, rs2235324, rs2413450 and rs5756506) and TF (rs3811647 and rs1799852), n = 1316. After controlling for inflammation, age and sex, we analysed the effects of carrying either single or multiple iron-lowering alleles on iron status. TMPRSS6 rs2235321 significantly affected plasma hepcidin concentrations (AA genotypes having lower hepcidin levels; F ratio 3.7, P = 0.014) with greater impact in individuals with low haemoglobin or ferritin. No other TMPRSS6 variant affected hepcidin. None of the TMPRSS6 variants nor a TMPRSS6 allele risk score affected other iron biomarkers or haematological traits. TF rs3811647 AA carriers had 21% higher transferrin (F ratio 16.0, P < 0.0001), 24% higher unsaturated iron-binding capacity (F ratio 12.8, P < 0.0001) and 25% lower transferrin saturation (F ratio 4.3, P < 0.0001) compared to GG carriers. TF rs3811647 was strongly associated with transferrin, unsaturated iron-binding capacity (UIBC) and transferrin saturation (TSAT) with a single allele effect of 8-12%. There was no association between either TF SNP and any haematological traits or iron biomarkers. We identified meaningful associations between TMPRSS6 rs2235321 and hepcidin and replicated the previous findings on the effects of TF rs3811647 on transferrin and iron binding capacity. However, the effects are subtle and contribute little to population variance. Further genetic and functional studies, including polymorphisms frequent in Africa populations, are needed to identify markers for genetically stratified approaches to prevention or treatment of iron deficiency anaemia.

Common Variants in the TMPRSS6 Gene Alter Hepcidin but not Plasma Iron in Response to Oral Iron in Healthy Gambian Adults: A Recall-by-Genotype Study

BACKGROUND

The role of genetic determinants in mediating iron status in Africans is not fully understood. Genome-wide association studies in non-African populations have revealed genetic variants in the transmembrane protease serine 6 gene (TMPRSS6) that are associated with the risk of anemia.

OBJECTIVES

To investigate the effects of risk alleles for low iron status, namely TMPRSS6 rs2235321, rs855791, and rs4820268, on responses to oral iron in healthy Gambian adults.

METHODS

Using a recall-by-genotype design, participants were selected from a pregenotype cohort of 3000 individuals in the Keneba Biobank (Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine). Participants were invited to participate in the study based on 9 genotype combinations obtained from 3 TMPRSS6 single nucleotide polymorphisms (SNPs): rs2235321, rs855791, and rs4820268. The participants fasted overnight and then ingested a single oral dose of ferrous sulfate (130 mg elemental iron). Blood samples were collected prior to iron ingestion and at 2 and 5 h after the oral iron dose. The effects of genotype on hepcidin and plasma iron parameters were assessed.

RESULTS

A total of 251 individuals were enrolled. Homozygous carriers of the major TMPRSS6 alleles at each of the SNPs had higher plasma hepcidin at baseline (rs2235321: GG compared with AA = 9.50 compared with 6.60 ng/ml, P = 0.035; rs855791: GG compared with AG = 9.50 compared with 4.96 ng/mL, P = 0.015; rs4820268: AA compared with GG = 9.50 compared with 3.27 ng/mL,  P = 0.002) and at subsequent timepoints. In most subjects, hepcidin concentrations increased following iron ingestion (overall group mean = 4.98 ± 0.98 ng/mL at 5 h, P < 0.001), but double heterozygotes at rs2235321 and rs855791 showed no increase (0.36 ± 0.40 ng/mL at 5 h, P = 0.667).

CONCLUSIONS

This study revealed that common TMPRSS6 variants influence hepcidin concentrations, but not iron status indicators either at baseline or following a large oral dose of iron. These results suggest that genetic variations in the TMPRSS6 gene are unlikely to be important contributors to variations in iron status in Africans.This study was registered at clinicaltrials.gov (# NCT03341338).

Low iron mitigates viral survival: insights from evolution, genetics, and pandemics-a review of current hypothesis

Background

Upon re-examination of our human history, evolutionary perspectives, and genetics, a prevailing iron deficiency phenotype appears to have evolved to protect the human race from extinction.

Body

In this review, we summarize the evolutionary and genetic perspectives pointing towards the hypothesis that low iron mitigates infection. The presence of infection promotes the generation of resistance alleles, and there are some evolutionary and genetic clues that suggest the presence of an iron deficiency phenotype that may have developed to protect against infection. Examples include the relative paucity of iron overload genes given the essential role of iron, as well as the persistence of iron deficiency among populations in spite of public health efforts to treat it. Additional examination of geographic areas with severe iron deficiency in the setting of pandemics including H1N1, SARS, and COVID-19 reveals that areas with higher prevalence of iron deficiency are less affected. RNA viruses have several evolutionary adaptations which suggest their absolute need for iron, and this dependency may be exploited during treatment.

Conclusion

RNA viruses pose a unique challenge to modern healthcare, with an average of 2-3 new pathogens being discovered yearly. Their overarching requirements for iron, along with human evolutionary and genetic adaptations which favored an iron deficiency phenotype, ultimately suggest the potential need for iron control in these infections.