Identifying genetic variants and pathways associated with extreme levels of fetal hemoglobin in sickle cell disease in Tanzania

Abstract

Background: Sickle cell disease (SCD) is a blood disorder caused by a point mutation on the beta globin gene resulting in the synthesis of abnormal hemoglobin. Fetal hemoglobin (HbF) reduces disease severity, but the levels vary from one individual to another. Most research has focused on common genetic variants which differ across populations and hence do not fully account for HbF variation. Methods: We investigated rare and common genetic variants that influence HbF levels in 14 SCD patients to elucidate variants and pathways in SCD patients with extreme HbF levels (≥7.7% for high HbF) and (≤2.5% for low HbF) in Tanzania. We performed targeted next generation sequencing (Illumina_Miseq) covering exonic and other significant fetal hemoglobin-associated loci, including BCL11A, MYB, HOXA9, HBB, HBG1, HBG2, CHD4, KLF1, MBD3, ZBTB7A and PGLYRP1. Results: Results revealed a range of genetic variants, including bi-allelic and multi-allelic SNPs, frameshift insertions and deletions, some of which have functional importance. Notably, there were significantly more deletions in individuals with high HbF levels (11% vs 0.9%). We identified frameshift deletions in individuals with high HbF levels and frameshift insertions in individuals with low HbF. CHD4 and MBD3 genes, interacting in the same sub-network, were identified to have a significant number of pathogenic or non-synonymous mutations in individuals with low HbF levels, suggesting an important role of epigenetic pathways in the regulation of HbF synthesis. Conclusions: This study provides new insights in selecting essential variants and identifying potential biological pathways associated with extreme HbF levels in SCD interrogating multiple genomic variants associated with HbF in SCD.

Prevalence of Hemoglobin-S and Baseline Level of Knowledge on Sickle Cell Disease Among Pregnant Women Attending Antenatal Clinics in Dar-Es-Salaam, Tanzania

“…Our study team at the Sickle Cell Programme, Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences (MUHAS) in Dar-es-Salaam has been at the forefront of conducting research on SCD in Tanzania. Over the years, research from our team has delineated various aspects including clinical epidemiology, health systems, research ethics, and genomic profiles of SCD in Tanzania ( Makani et al, 2011 ; Costa et al, 2021 ; Jacob et al, 2020 ; Bukini et al, 2020 ; Masamu et al, 2020 ; Nkya et al, 2020 ; Urio et al, 2020 ). Since 2017, the Sickle Cell Programme is part of the SickleInAfrica consortium, funded by the United States National Institutes of Health (NIH) through the National Heart, Lung and Blood Institute (NHLBI), with the aims to foster connectedness among stakeholders, develop an electronic database of patients, advance standards of care, provide training, and conduct research on pertinent areas on SCD in the sub-Saharan African context ( Makani et al, 2020 ).…”

Developing a Sustainable Cardiovascular Disease Research Strategy in Tanzania Through Training: Leveraging From the East African Centre of Excellence in Cardiovascular Sciences Project

“…In South Africa, for example, it was recently shown that a gene panel with a yield of >60% in a European population has a yield of only 18% in South Africans with hypertrophic cardiomyopathy (55). In Tanzania, much of the reports on genetic studies have been on sickle cell anemia and malaria (56,57), as well as on-going research on rare disease conditions. This agenda will focus to put in place infrastructure in terms of resources and human capacity build-up to be able to host a wide range of genetic research on CVD.…”

Exome sequencing in high and low fetal haemoglobin Arab–Indian haplotype sickle cell disease

“…Our results differ from those of Nkya et al . who studied 14 Tanzanian sickle cell anaemia patients with high ( n = 9, HbF 15–32%) or low HbF ( n = 5; HbF 0·3–2·2%) and found an increased number of pathogenic or non‐synonymous mutations in CHD4 (chromodomain helicase DNA binding protein) in the low‐HbF group 11 . CHD4 is a component of the NuRD (nucleosome remodeling and deacetylase) complex, a transcriptional repressor.…”