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Adjemout M, Gallardo F, Torres M, Thiam A, Mbengue B, Dieye A, Marquet S, Rihet P. From Genome-wide Association Studies to Functional Variants: ARL14 Cis-regulatory Variants Are Associated With Severe Malaria. J Infect Dis 2024; 230:e743-e752. [PMID: 38531688 DOI: 10.1093/infdis/jiae159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Genome-wide association studies have identified several nonfunctional tag single-nucleotide polymorphisms (SNPs) associated with severe malaria. We hypothesized that causal SNPs could play a significant role in severe malaria by altering promoter or enhancer activity. Here, we sought to identify such regulatory SNPs. METHODS SNPs in linkage disequilibrium with tagSNPs associated with severe malaria were identified and were further annotated using FUMA. Then, SNPs were prioritized using the integrative weighted scoring method to identify regulatory ones. Gene reporter assays were performed to assess the regulatory effect of a region containing candidates. The association between SNPs and severe malaria was assessed using logistic regression models in a Senegalese cohort. RESULTS Among 418 SNPs, the best candidates were rs116525449 and rs79644959, which were in full disequilibrium between them, and located within the ARL14 promoter. Our gene reporter assay results revealed that the region containing the SNPs exhibited cell-specific promoter or enhancer activity, while the SNPs influenced promoter activity. We detected an association between severe malaria and those 2 SNPs using the overdominance model and we replicated the association of severe malaria with the tagSNP rs116423146. CONCLUSIONS We suggest that these SNPs regulate ARL14 expression in immune cells and the presentation of antigens to T lymphocytes, thus influencing severe malaria development.
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Affiliation(s)
- Mathieu Adjemout
- Aix-Marseille Univ, Inserm, TAGC Theories and Approaches of Genomic Complexity, MarMaRa Institute, Marseille, France
| | - Frederic Gallardo
- Aix-Marseille Univ, Inserm, TAGC Theories and Approaches of Genomic Complexity, MarMaRa Institute, Marseille, France
| | - Magali Torres
- Aix-Marseille Univ, Inserm, TAGC Theories and Approaches of Genomic Complexity, MarMaRa Institute, Marseille, France
| | - Alassane Thiam
- Pole d'Immunophysiopathologie & Maladies Infectieuses, Institut Pasteur de Dakar
| | - Babacar Mbengue
- Service d'Immunologie, Université Cheikh Anta Diop de Dakar, Senegal
| | - Alioune Dieye
- Service d'Immunologie, Université Cheikh Anta Diop de Dakar, Senegal
| | - Sandrine Marquet
- Aix-Marseille Univ, Inserm, TAGC Theories and Approaches of Genomic Complexity, MarMaRa Institute, Marseille, France
| | - Pascal Rihet
- Aix-Marseille Univ, Inserm, TAGC Theories and Approaches of Genomic Complexity, MarMaRa Institute, Marseille, France
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2
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Hu X, Wang J, Yang K, Fan H, Wu J, Ren J, Han G, Li J, Xue Z, Liu X, Lv X. The GWAS SNP rs80207740 modulates erythrocyte traits via allele-specific binding of IKZF1 and targeting XPO7 gene. FASEB J 2024; 38:e23666. [PMID: 38780091 DOI: 10.1096/fj.202302017r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 03/31/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Genome-wide association studies have identified many single nucleotide polymorphisms (SNPs) associated with erythrocyte traits. However, the functional variants and their working mechanisms remain largely unknown. Here, we reported that the SNP of rs80207740, which was associated with red blood cell (RBC) volume and hemoglobin content across populations, conferred enhancer activity to XPO7 gene via allele-differentially binding to Ikaros family zinc finger 1 (IKZF1). We showed that the region around rs80207740 was an erythroid-specific enhancer using reporter assays, and that the G-allele further enhanced activity. 3D genome evidence showed that the enhancer interacted with the XPO7 promoter, and eQTL analysis suggested that the G-allele upregulated expression of XPO7. We further showed that the rs80207740-G allele facilitated the binding of transcription factor IKZF1 in EMSA and ChIP analyses. Knockdown of IKZF1 and GATA1 resulted in decreased expression of Xpo7 in both human and mouse erythroid cells. Finally, we constructed Xpo7 knockout mouse by CRISPR/Cas9 and observed anemic phenotype with reduced volume and hemoglobin content of RBC, consistent to the effect of rs80207740 on erythrocyte traits. Overall, our study demonstrated that rs80207740 modulated erythroid indices by regulating IKZF1 binding and Xpo7 expression.
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Affiliation(s)
- Xinjun Hu
- State Key Laboratory of Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Jiaxin Wang
- State Key Laboratory of Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Ke Yang
- State Key Laboratory of Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Hong Fan
- State Key Laboratory of Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Jie Wu
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Jiuqiang Ren
- State Key Laboratory of Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Gaijing Han
- State Key Laboratory of Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Jing Li
- State Key Laboratory of Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Zheng Xue
- State Key Laboratory of Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xuehui Liu
- State Key Laboratory of Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xiang Lv
- State Key Laboratory of Complex, Severe, and Rare Diseases, Haihe Laboratory of Cell Ecosystem, Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
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3
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Skok Gibbs C, Mahmood O, Bonneau R, Cho K. PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization. Genome Biol 2024; 25:88. [PMID: 38589899 PMCID: PMC11003171 DOI: 10.1186/s13059-024-03226-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present Probabilistic Matrix Factorization for Gene Regulatory Network Inference (PMF-GRN). Using single-cell expression data, PMF-GRN infers latent factors capturing transcription factor activity and regulatory relationships. Using variational inference allows hyperparameter search for principled model selection and direct comparison to other generative models. We extensively test and benchmark our method using real single-cell datasets and synthetic data. We show that PMF-GRN infers GRNs more accurately than current state-of-the-art single-cell GRN inference methods, offering well-calibrated uncertainty estimates.
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Affiliation(s)
| | - Omar Mahmood
- Center for Data Science, New York University, New York, NY, 10011, USA
| | - Richard Bonneau
- Center for Data Science, New York University, New York, NY, 10011, USA
- Prescient Design, Genentech, New York, NY, 10010, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Kyunghyun Cho
- Center for Data Science, New York University, New York, NY, 10011, USA.
- Prescient Design, Genentech, New York, NY, 10010, USA.
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4
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Naffa R, Hegedűs L, Hegedűs T, Tóth S, Papp B, Tordai A, Enyedi Á. Plasma membrane Ca 2+ pump isoform 4 function in cell migration and cancer metastasis. J Physiol 2024; 602:1551-1564. [PMID: 36876504 DOI: 10.1113/jp284179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/02/2023] [Indexed: 03/07/2023] Open
Abstract
The Ca2+ ion is a universal second messenger involved in many vital physiological functions including cell migration and development. To fulfil these tasks the cytosolic Ca2+ concentration is tightly controlled, and this involves an intricate functional balance between a variety of channels and pumps of the Ca2+ signalling machinery. Among these proteins, plasma membrane Ca2+ ATPases (PMCAs) represent the major high-affinity Ca2+ extrusion systems in the cell membrane that are effective in maintaining free Ca2+ concentration at exceedingly low cytosolic levels, which is essential for normal cell function. An imbalance in Ca2+ signalling can have pathogenic consequences including cancer and metastasis. Recent studies have highlighted the role of PMCAs in cancer progression and have shown that a particular variant, PMCA4b, is downregulated in certain cancer types, causing delayed attenuation of the Ca2+ signal. It has also been shown that loss of PMCA4b leads to increased migration and metastasis of melanoma and gastric cancer cells. In contrast, an increased PMCA4 expression has been reported in pancreatic ductal adenocarcinoma that coincided with increased cell migration and shorter patient survival, suggesting distinct roles of PMCA4b in various tumour types and/or different stages of tumour development. The recently discovered interaction of PMCAs with basigin, an extracellular matrix metalloproteinase inducer, may provide further insights into our understanding of the specific roles of PMCA4b in tumour progression and cancer metastasis.
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Affiliation(s)
- Randa Naffa
- Molecular Biology Research Laboratory, School of Medicine, The University of Jordan, Amman, Jordan
| | - Luca Hegedűs
- Department of Thoracic Surgery, Ruhrlandklinik, University Clinic Essen, Essen, Germany
| | - Tamás Hegedűs
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- ELKH-SE Biophysical Virology Research Group, Eötvös Loránd Research Network, Budapest, Hungary
| | - Sarolta Tóth
- Department of Transfusion Medicine, Semmelweis University, Budapest, Hungary
| | - Béla Papp
- Institut National de la Santé et de la Recherche Médicale, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, Paris, France
- Institut de Recherche Saint-Louis, Hôpital Saint-Louis, Université de Paris, Paris, France
- CEA, DRF-Institut Francois Jacob, Department of Hemato-Immunology Research, Hôpital Saint-Louis, Paris, France
| | - Attila Tordai
- Department of Transfusion Medicine, Semmelweis University, Budapest, Hungary
| | - Ágnes Enyedi
- ELKH-SE Biophysical Virology Research Group, Eötvös Loránd Research Network, Budapest, Hungary
- Department of Transfusion Medicine, Semmelweis University, Budapest, Hungary
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5
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Pance A, Ng BL, Mwikali K, Koutsourakis M, Agu C, Rouhani FJ, Montandon R, Law F, Ponstingl H, Rayner JC. Novel stem cell technologies are powerful tools to understand the impact of human factors on Plasmodium falciparum malaria. Front Cell Infect Microbiol 2023; 13:1287355. [PMID: 38173794 PMCID: PMC10762799 DOI: 10.3389/fcimb.2023.1287355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Plasmodium falciparum parasites have a complex life cycle, but the most clinically relevant stage of the disease is the invasion of erythrocytes and the proliferation of the parasite in the blood. The influence of human genetic traits on malaria has been known for a long time, however understanding the role of the proteins involved is hampered by the anuclear nature of erythrocytes that makes them inaccessible to genetic tools. Here we overcome this limitation using stem cells to generate erythroid cells with an in-vitro differentiation protocol and assess parasite invasion with an adaptation of flow cytometry to detect parasite hemozoin. We combine this strategy with reprogramming of patient cells to Induced Pluripotent Stem Cells and genome editing to understand the role of key genes and human traits in malaria infection. We show that deletion of basigin ablates invasion while deletion of ATP2B4 has a minor effect and that erythroid cells from reprogrammed patient-derived HbBart α-thalassemia samples poorly support infection. The possibility to obtain patient-secific and genetically modifed erythoid cells offers an unparalleled opportunity to study the role of human genes and polymorphisms in malaria allowing preservation of the genomic background to demonstrate their function and understand their mechanisms.
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Affiliation(s)
- Alena Pance
- Wellcome Sanger Institute, Cambridge, United Kingdom
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Bee L. Ng
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Kioko Mwikali
- Wellcome Sanger Institute, Cambridge, United Kingdom
- Bioscience Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Chukwuma Agu
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Ruddy Montandon
- Wellcome Sanger Institute, Cambridge, United Kingdom
- Wellcome Centre of Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Frances Law
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | - Julian C. Rayner
- Wellcome Sanger Institute, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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6
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Almojil D, Diawara A, Soulama I, Dieng MM, Manikandan V, Sermé SS, Sombié S, Diarra A, Barry A, Coulibaly SA, Sirima SB, Idaghdour Y. Impact of Plasmodium falciparum infection on DNA methylation of circulating immune cells. Front Genet 2023; 14:1197933. [PMID: 37470040 PMCID: PMC10352500 DOI: 10.3389/fgene.2023.1197933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/02/2023] [Indexed: 07/21/2023] Open
Abstract
The regulation of immune cell responses to infection is a complex process that involves various molecular mechanisms, including epigenetic regulation. DNA methylation has been shown to play central roles in regulating gene expression and modulating cell response during infection. However, the nature and extent to which DNA methylation is involved in the host immune response in human malaria remains largely unknown. Here, we present a longitudinal study investigating the temporal dynamics of genome-wide in vivo DNA methylation profiles using 189 MethylationEPIC 850 K profiles from 66 children in Burkina Faso, West Africa, sampled three times: before infection, during symptomatic parasitemia, and after malaria treatment. The results revealed major changes in the DNA methylation profiles of children in response to both Plasmodium falciparum infection and malaria treatment, with widespread hypomethylation of CpGs upon infection (82% of 6.8 K differentially methylated regions). We document a remarkable reversal of CpG methylation profiles upon treatment to pre-infection states. These changes implicate divergence in core immune processes, including the regulation of lymphocyte, neutrophil, and myeloid leukocyte function. Integrative DNA methylation-mRNA analysis of a top differentially methylated region overlapping the pro-inflammatory gene TNF implicates DNA methylation of TNF cis regulatory elements in the molecular mechanisms of TNF regulation in human malaria. Our results highlight a central role of epigenetic regulation in mounting the host immune response to P. falciparum infection and in response to malaria treatment.
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Affiliation(s)
- Dareen Almojil
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Aïssatou Diawara
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Issiaka Soulama
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Mame Massar Dieng
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Vinu Manikandan
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Samuel S. Sermé
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Salif Sombié
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Amidou Diarra
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Aissata Barry
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | | | - Sodiomon B. Sirima
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Youssef Idaghdour
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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7
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Li M, Wang D, Liu Z, Huang Y, Zhang Q, Pan C, Lin Y, Sun L, Zheng Y. Assessing the effects of aging on the renal endothelial cell landscape using single-cell RNA sequencing. Front Genet 2023; 14:1175716. [PMID: 37214419 PMCID: PMC10196692 DOI: 10.3389/fgene.2023.1175716] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Endothelial cells (ECs) with senescence-associated secretory phenotypes (SASP) have been identified as a key mechanism of aging that contributes to various age-related kidney diseases. In this study, we used single-cell RNA sequencing (scRNA-seq) to create a transcriptome atlas of murine renal ECs and identify transcriptomic changes that occur during aging. We identified seven different subtypes of renal ECs, with glomerular ECs and angiogenic ECs being the most affected by senescence. We confirmed our scRNA-seq findings by using double immunostaining for an EC marker (CD31) and markers of specialized EC phenotypes. Our analysis of the dynamics of capillary lineage development revealed a chronic state of inflammation and compromised glomerular function as prominent aging features. Additionally, we observed an elevated pro-inflammatory and pro-coagulant microenvironment in aged glomerular ECs, which may contribute to age-related glomerulosclerosis and renal fibrosis. Through intercellular communication analysis, we also identified changes in signaling involved in immune regulation that may contribute to a hostile microenvironment for renal homeostasis and function. Overall, our findings provide new insights into the mechanisms of aging in the renal endothelium and may pave the way for the discovery of diagnostic biomarkers and therapeutic interventions against age-related kidney diseases.
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Affiliation(s)
- Mengke Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, China
| | - Dongliang Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Zhong Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yanjing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qikai Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Caineng Pan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yuheng Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Li Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yingfeng Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
- Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, China
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Thiam A, Nisar S, Adjemout M, Gallardo F, Ka O, Mbengue B, Diop G, Dieye A, Marquet S, Rihet P. ATP2B4 regulatory genetic variants are associated with mild malaria. Malar J 2023; 22:68. [PMID: 36849945 PMCID: PMC9972758 DOI: 10.1186/s12936-023-04503-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/18/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Genome-wide association studies have identified ATP2B4 as a severe malaria resistance gene. Recently, 8 potential causal regulatory variants have been shown to be associated with severe malaria. METHODS Genotyping of rs10900585, rs11240734, rs1541252, rs1541253, rs1541254, rs1541255, rs10751450, rs10751451 and rs10751452 was performed in 154 unrelated individuals (79 controls and 75 mild malaria patients). rs10751450, rs10751451 and rs10751452 were genotyped by Taqman assays, whereas the fragment of the ATP2B4 gene containing the remaining SNPs was sequenced. Logistic regression analysis was used to assess the association between the SNPs and mild malaria. RESULTS The results showed that mild malaria was associated with rs10900585, rs11240734, rs1541252, rs1541253, rs1541254, rs1541255, rs10751450, rs10751451 and rs10751452. The homozygous genotypes for the major alleles were associated with an increased risk of mild malaria. Furthermore, the haplotype containing the major alleles and that containing the minor alleles were the most frequent haplotypes. Individuals with the major haplotypes had a significantly higher risk of mild malaria compared to the carriers of the minor allele haplotype. CONCLUSIONS ATP2B4 polymorphisms that have been associated with severe malaria are also associated with mild malaria.
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Affiliation(s)
- Alassane Thiam
- grid.418508.00000 0001 1956 9596Unité d’Immunogénétique, Institut Pasteur de Dakar, Dakar, Senegal
| | - Samia Nisar
- grid.5399.60000 0001 2176 4817Aix Marseille Univ, INSERM, TAGC, MarMaRa Institute, Marseille, France ,grid.444997.30000 0004 1761 3137Sardar Bahadur Khan Women’s University, Quetta, 1800 Balochistan Pakistan
| | - Mathieu Adjemout
- grid.5399.60000 0001 2176 4817Aix Marseille Univ, INSERM, TAGC, MarMaRa Institute, Marseille, France
| | - Frederic Gallardo
- grid.5399.60000 0001 2176 4817Aix Marseille Univ, INSERM, TAGC, MarMaRa Institute, Marseille, France
| | - Oumar Ka
- grid.8191.10000 0001 2186 9619Service d’Immunologie, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | - Babacar Mbengue
- grid.8191.10000 0001 2186 9619Service d’Immunologie, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | - Gora Diop
- grid.418508.00000 0001 1956 9596Unité d’Immunogénétique, Institut Pasteur de Dakar, Dakar, Senegal
| | - Alioune Dieye
- grid.8191.10000 0001 2186 9619Service d’Immunologie, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | - Sandrine Marquet
- Aix Marseille Univ, INSERM, TAGC, MarMaRa Institute, Marseille, France.
| | - Pascal Rihet
- Aix Marseille Univ, INSERM, TAGC, MarMaRa Institute, Marseille, France.
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9
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Joof F, Hartmann E, Jarvis A, Colley A, Cross JH, Avril M, Prentice AM, Cerami C. Genetic variations in human ATP2B4 gene alter Plasmodium falciparum in vitro growth in RBCs from Gambian adults. Malar J 2023; 22:5. [PMID: 36604655 PMCID: PMC9817369 DOI: 10.1186/s12936-022-04359-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 11/03/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Polymorphisms in ATP2B4 coding for PMCA4b, the primary regulator of erythrocyte calcium concentration, have been shown by GWAS and cross-sectional studies to protect against severe malaria but the mechanism remains unknown. METHODS Using a recall-by-genotype design, we investigated the impact of a common haplotype variant in ATP2B4 using in vitro assays that model erythrocyte stage malaria pathogenesis. Ninety-six donors representing homozygote (carriers of the minor allele, C/C), heterozygote (T/C) and wildtype (T/T) carriers of the tagging SNP rs1541252 were selected from a cohort of over 12,000 participants in the Keneba Biobank. RESULTS Red blood cells (RBCs) from homozygotes showed reduced PMCA4b protein expression (mean fluorescence intensities (MFI = 2428 ± 124, 3544 ± 159 and 4261 ± 283], for homozygotes, heterozygotes and wildtypes respectively, p < 0.0001) and slower rates of calcium expulsion (calcium t½ ± SD = 4.7 ± 0.5, 1.8 ± 0.3 and 1.9 ± 0.4 min, p < 0.0001). Growth of a Plasmodium falciparum laboratory strain (FCR3) and two Gambian field isolates was decreased in RBCs from homozygotes compared to heterozygotes and wildtypes (p < 0.01). Genotype group did not affect parasite adhesion in vitro or var-gene expression in malaria-infected RBCs. Parasite growth was inhibited by a known inhibitor of PMCA4b, aurintricarboxylic acid (IC50 = 122uM CI: 110-134) confirming its sensitivity to calcium channel blockade. CONCLUSION The data support the hypothesis that this ATP2B4 genotype, common in The Gambia and other malaria-endemic areas, protects against severe malaria through the suppression of parasitaemia during an infection. Reduction in parasite density plays a pivotal role in disease outcome by minimizing all aspects of malaria pathogenesis. Follow up studies are needed to further elucidate the mechanism of protection and to determine if this ATP2B4 genotype carries a fitness cost or increases susceptibility to other human disease.
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Affiliation(s)
- Fatou Joof
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | | | | | - Alhassan Colley
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - James H Cross
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | | | - Andrew M Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia.
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10
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Ren D, Liu R, Yan X, Zhang Q, Zeng X, Yuan X. Intensive stretch-activated CRT-PMCA1 feedback loop promoted apoptosis of myoblasts through Ca 2+ overloading. Apoptosis 2022; 27:929-945. [PMID: 35976579 DOI: 10.1007/s10495-022-01759-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2022] [Indexed: 11/29/2022]
Abstract
Mechanical stretch exerted pro-apoptotic effect on myoblasts, the mechanism of which is currently unknown. Intracellular Ca2+ accumulation has been implicated in stretch-induced apoptosis. calreticulin (CRT) and plasma membrane Ca2+ transporting ATPase 1 (PMCA1) are two critical components of Ca2+ signaling system participating in intracellular Ca2+ homeostasis. In this study, we explored the contribution of CRT and PMCA1 in mediating stretch-induced Ca2+ accumulation and apoptosis of myoblasts. Stretching stimuli elevated level of CRT while inhibited activity of PMCA1. Moreover, there were bidirectional regulations between CRT and PMCA1, which formed the positive feedback loop leading to continuous increment of CRT level and repression of PMCA1 activity, in stretched myoblasts. Specifically, increased CRT level inhibited PMCA1 activity via suppressing Calmodulin (CaM), while reduced PMCA1 activity promoted CRT expression through activating p38MAPK pathway. Thus, the CRT-CaM-PMCA1 and PMCA1-p38MAPK-CRT pathways constituted a close cycle comprising CRT, PMCA1, CaM and p38MAPK. Inhibition of both CaM and p38MAPK affected the other three factors in stretched myoblasts. Circulation of the vicious cycle resulted in escalated Ca2+ overloading in myoblasts under continuous stretching stimuli. CRT knock-down, PMCA1 overexpression, and p38MAPK inhibition all attenuated the raised intracellular Ca2+ level and ameliorated myoblast apoptosis in the stretching environment. Conversely, CRT overexpression, PMCA1 knock-down, and CaM inhibition all aggravated stretch-induced Ca2+ overloading and myoblast apoptosis. A positive feedback loop between CRT and PMCA1 was activated in stretched myoblasts, which contributed to intracellular Ca2+ accumulation and resultant myoblast apoptosis.
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Affiliation(s)
- Dapeng Ren
- Department of Stomatology Medical Center, Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Central Laboratory of Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Department of Orthodontics, School of Stomatology, Qingdao University, Qingdao, China
| | - Ran Liu
- Department of Stomatology Medical Center, Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Central Laboratory of Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Xiao Yan
- Department of Stomatology Medical Center, Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Central Laboratory of Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Department of Orthodontics, School of Stomatology, Qingdao University, Qingdao, China
| | - Qiang Zhang
- Department of Stomatology Medical Center, Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Central Laboratory of Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Department of Orthodontics, School of Stomatology, Qingdao University, Qingdao, China
| | - Xuemin Zeng
- Department of Stomatology Medical Center, Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Central Laboratory of Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.,Department of Orthodontics, School of Stomatology, Qingdao University, Qingdao, China
| | - Xiao Yuan
- Department of Stomatology Medical Center, Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China. .,Central Laboratory of Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China. .,Department of Orthodontics, School of Stomatology, Qingdao University, Qingdao, China.
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11
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Asih PBS, Siregar JE, Dewayanti FK, Pravitasari NE, Rozi IE, Rizki AFM, Risandi R, Couper KN, Oceandy D, Syafruddin D. Treatment with specific and pan-plasma membrane calcium ATPase (PMCA) inhibitors reduces malaria parasite growth in vitro and in vivo. Malar J 2022; 21:206. [PMID: 35768835 PMCID: PMC9241181 DOI: 10.1186/s12936-022-04228-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/17/2022] [Indexed: 11/22/2022] Open
Abstract
Background Rapid emergence of Plasmodium resistance to anti-malarial drug mainstays has driven a continual effort to discover novel drugs that target different biochemical pathway (s) during infection. Plasma membrane Calcium + 2 ATPase (PMCA4), a novel plasma membrane protein that regulates Calcium levels in various cells, namely red blood cell (RBC), endothelial cell and platelets, represents a new biochemical pathway that may interfere with susceptibility to malaria and/or severe malaria. Methods This study identified several pharmacological inhibitors of PMCA4, namely ATA and Resveratrol, and tested for their anti-malarial activities in vitro and in vivo using the Plasmodium falciparum 3D7 strain, the Plasmodium berghei ANKA strain, and Plasmodium yoelii 17XL strain as model. Results In vitro propagation of P. falciparum 3D7 strain in the presence of a wide concentration range of the inhibitors revealed that the parasite growth was inhibited in a dose-dependent manner, with IC50s at 634 and 0.231 µM, respectively. Results The results confirmed that both compounds exhibit moderate to potent anti-malarial activities with the strongest parasite growth inhibition shown by resveratrol at 0.231 µM. In vivo models using P. berghei ANKA for experimental cerebral malaria and P. yoelii 17XL for the effect on parasite growth, showed that the highest dose of ATA, 30 mg/kg BW, increased survival of the mice. Likewise, resveratrol inhibited the parasite growth following 4 days intraperitoneal injection at the dose of 100 mg/kg BW. Conclusion The findings indicate that the PMCA4 of the human host may be a potential target for novel anti-malarials, either as single drug or in combination with the currently available effective anti-malarials.
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Affiliation(s)
- Puji B S Asih
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Josephine E Siregar
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Farahana K Dewayanti
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Normalita E Pravitasari
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Ismail E Rozi
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Andita F M Rizki
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Rifqi Risandi
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia
| | - Kevin N Couper
- Division of Infection, Immunity & Respiratory Medicine, The University of Manchester, Manchester, UK
| | - Delvac Oceandy
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, UK
| | - Din Syafruddin
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta, Indonesia. .,Department of Parasitology, Faculty of Medicine, Hasanuddin University, Makassar, Indonesia.
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12
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Uyoga S, Watson JA, Wanjiku P, Rop JC, Makale J, Macharia AW, Kariuki SN, Nyutu GM, Shebe M, Mosobo M, Mturi N, Rockett KA, Woodrow CJ, Dondorp AM, Maitland K, White NJ, Williams TN. The impact of malaria-protective red blood cell polymorphisms on parasite biomass in children with severe Plasmodium falciparum malaria. Nat Commun 2022; 13:3307. [PMID: 35676275 PMCID: PMC9178016 DOI: 10.1038/s41467-022-30990-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/24/2022] [Indexed: 11/08/2022] Open
Abstract
Severe falciparum malaria is a major cause of preventable child mortality in sub-Saharan Africa. Plasma concentrations of P. falciparum Histidine-Rich Protein 2 (PfHRP2) have diagnostic and prognostic value in severe malaria. We investigate the potential use of plasma PfHRP2 and the sequestration index (the ratio of PfHRP2 to parasite density) as quantitative traits for case-only genetic association studies of severe malaria. Data from 2198 Kenyan children diagnosed with severe malaria, genotyped for 14 major candidate genes, show that polymorphisms in four major red cell genes that lead to hemoglobin S, O blood group, α-thalassemia, and the Dantu blood group, are associated with substantially lower admission plasma PfHRP2 concentrations, consistent with protective effects against extensive parasitized erythrocyte sequestration. In contrast the known protective ATP2B4 polymorphism is associated with higher plasma PfHRP2 concentrations, lower parasite densities and a higher sequestration index. We provide testable hypotheses for the mechanism of protection of ATP2B4.
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Affiliation(s)
- S Uyoga
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
| | - J A Watson
- Mahidol-Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - P Wanjiku
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - J C Rop
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - J Makale
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - A W Macharia
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - S N Kariuki
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - G M Nyutu
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - M Shebe
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - M Mosobo
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - N Mturi
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - K A Rockett
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - C J Woodrow
- Mahidol-Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - A M Dondorp
- Mahidol-Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - K Maitland
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Surgery and Cancer, Institute of Global Health Innovation, Imperial College, London, UK
| | - N J White
- Mahidol-Oxford Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - T N Williams
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
- Department of Surgery and Cancer, Institute of Global Health Innovation, Imperial College, London, UK.
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13
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Introini V, Govendir MA, Rayner JC, Cicuta P, Bernabeu M. Biophysical Tools and Concepts Enable Understanding of Asexual Blood Stage Malaria. Front Cell Infect Microbiol 2022; 12:908241. [PMID: 35711656 PMCID: PMC9192966 DOI: 10.3389/fcimb.2022.908241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/27/2022] [Indexed: 12/02/2022] Open
Abstract
Forces and mechanical properties of cells and tissues set constraints on biological functions, and are key determinants of human physiology. Changes in cell mechanics may arise from disease, or directly contribute to pathogenesis. Malaria gives many striking examples. Plasmodium parasites, the causative agents of malaria, are single-celled organisms that cannot survive outside their hosts; thus, thost-pathogen interactions are fundamental for parasite’s biological success and to the host response to infection. These interactions are often combinations of biochemical and mechanical factors, but most research focuses on the molecular side. However, Plasmodium infection of human red blood cells leads to changes in their mechanical properties, which has a crucial impact on disease pathogenesis because of the interaction of infected red blood cells with other human tissues through various adhesion mechanisms, which can be probed and modelled with biophysical techniques. Recently, natural polymorphisms affecting red blood cell biomechanics have also been shown to protect human populations, highlighting the potential of understanding biomechanical factors to inform future vaccines and drug development. Here we review biophysical techniques that have revealed new aspects of Plasmodium falciparum invasion of red blood cells and cytoadhesion of infected cells to the host vasculature. These mechanisms occur differently across Plasmodium species and are linked to malaria pathogenesis. We highlight promising techniques from the fields of bioengineering, immunomechanics, and soft matter physics that could be beneficial for studying malaria. Some approaches might also be applied to other phases of the malaria lifecycle and to apicomplexan infections with complex host-pathogen interactions.
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Affiliation(s)
- Viola Introini
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Viola Introini,
| | - Matt A. Govendir
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain
| | - Julian C. Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Pietro Cicuta
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Maria Bernabeu
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain
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14
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Sánchez-Arcila JC, Jensen KDC. Forward Genetics in Apicomplexa Biology: The Host Side of the Story. Front Cell Infect Microbiol 2022; 12:878475. [PMID: 35646724 PMCID: PMC9133346 DOI: 10.3389/fcimb.2022.878475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/31/2022] [Indexed: 11/13/2022] Open
Abstract
Forward genetic approaches have been widely used in parasitology and have proven their power to reveal the complexities of host-parasite interactions in an unbiased fashion. Many aspects of the parasite's biology, including the identification of virulence factors, replication determinants, antibiotic resistance genes, and other factors required for parasitic life, have been discovered using such strategies. Forward genetic approaches have also been employed to understand host resistance mechanisms to parasitic infection. Here, we will introduce and review all forward genetic approaches that have been used to identify host factors involved with Apicomplexa infections, which include classical genetic screens and QTL mapping, GWAS, ENU mutagenesis, overexpression, RNAi and CRISPR-Cas9 library screens. Collectively, these screens have improved our understanding of host resistance mechanisms, immune regulation, vaccine and drug designs for Apicomplexa parasites. We will also discuss how recent advances in molecular genetics give present opportunities to further explore host-parasite relationships.
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Affiliation(s)
- Juan C. Sánchez-Arcila
- Department of Molecular and Cell Biology, University of California Merced, Merced, CA, United States
| | - Kirk D. C. Jensen
- Department of Molecular and Cell Biology, University of California Merced, Merced, CA, United States
- Health Science Research Institute, University of California, Merced, Merced, CA, United States
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15
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Identification of ATP2B4 Regulatory Element Containing Functional Genetic Variants Associated with Severe Malaria. Int J Mol Sci 2022; 23:ijms23094849. [PMID: 35563239 PMCID: PMC9101746 DOI: 10.3390/ijms23094849] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/15/2022] [Accepted: 04/22/2022] [Indexed: 12/04/2022] Open
Abstract
Genome-wide association studies for severe malaria (SM) have identified 30 genetic variants mostly located in non-coding regions. Here, we aimed to identify potential causal genetic variants located in these loci and demonstrate their functional activity. We systematically investigated the regulatory effect of the SNPs in linkage disequilibrium (LD) with the malaria-associated genetic variants. Annotating and prioritizing genetic variants led to the identification of a regulatory region containing five ATP2B4 SNPs in LD with rs10900585. We found significant associations between SM and rs10900585 and our candidate SNPs (rs11240734, rs1541252, rs1541253, rs1541254, and rs1541255) in a Senegalese population. Then, we demonstrated that both individual SNPs and the combination of SNPs had regulatory effects. Moreover, CRISPR/Cas9-mediated deletion of this region decreased ATP2B4 transcript and protein levels and increased Ca2+ intracellular concentration in the K562 cell line. Our data demonstrate that severe malaria-associated genetic variants alter the expression of ATP2B4 encoding a plasma membrane calcium-transporting ATPase 4 (PMCA4) expressed on red blood cells. Altering the activity of this regulatory element affects the risk of SM, likely through calcium concentration effect on parasitaemia.
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16
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Groomes PV, Kanjee U, Duraisingh MT. RBC membrane biomechanics and Plasmodium falciparum invasion: probing beyond ligand-receptor interactions. Trends Parasitol 2022; 38:302-315. [PMID: 34991983 PMCID: PMC8917059 DOI: 10.1016/j.pt.2021.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 10/19/2022]
Abstract
A critical step in malaria blood-stage infections is the invasion of red blood cells (RBCs) by merozoite forms of the Plasmodium parasite. Much progress has been made in defining the parasite ligands and host receptors that mediate this critical step. However, less well understood are the RBC biophysical determinants that influence parasite invasion. In this review we explore how Plasmodium falciparum merozoites interact with the RBC membrane during invasion to modulate RBC deformability and facilitate invasion. We further highlight RBC biomechanics-related polymorphisms that might have been selected for in human populations due to their ability to reduce parasite invasion. Such an understanding will reveal the translational potential of targeting host pathways affecting RBC biomechanical properties for the treatment of malaria.
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Affiliation(s)
- Patrice V Groomes
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Usheer Kanjee
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Manoj T Duraisingh
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
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17
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Miyasaka Y, Niwa S, Masuya T, Ishii R, Kobayashi M, Horio F, Ohno T. E3 ubiquitin ligase RNF123-deficient mice exhibit reduced parasitemia and mortality in rodent malaria (Plasmodium yoelii 17XL) infection. Parasitol Int 2022; 88:102542. [PMID: 35063657 DOI: 10.1016/j.parint.2022.102542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/22/2021] [Accepted: 01/12/2022] [Indexed: 11/19/2022]
Abstract
Increased levels of several human ubiquitin ligases, including ring finger protein 123 (RNF123), in red blood cells with Plasmodium falciparum infection, have been reported. RNF123 is an E3 ubiquitin ligase that is highly expressed in erythroid cells. However, the function of the RNF123 gene and the relationship between the RNF123 gene and malarial parasite has not been clarified in vivo. In this study, we generated RNF123-deficient mice using the CRISPR/Cas9 system, and analyzed malaria susceptibility and erythrocyte morphology. The levels of parasitemia 5 days post-infection and mortality 21 days post-infection with the lethal type of rodent malaria (Plasmodium yoelii 17XL) in RNF123-deficient mice was significantly lower than that in wild-type mice. In contrast, red blood cell morphology in RNF123-deficient mice was almost normal. These results suggest that erythrocytic RNF123 plays a role in susceptibility to rodent malaria infection, but does not play a role in erythrocyte morphology.
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Affiliation(s)
- Yuki Miyasaka
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Shota Niwa
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Tomomi Masuya
- Department of Applied Molecular Bioscience, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Reika Ishii
- Department of Applied Molecular Bioscience, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Misato Kobayashi
- Department of Applied Molecular Bioscience, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan; Department of Nutritional Sciences, Nagoya University of Arts and Sciences, 57 Takenoyama, Iwasaki-cho, Nisshin, Aichi 470-0196, Japan
| | - Fumihiko Horio
- Department of Applied Molecular Bioscience, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan; Department of Life Studies and Environmental Science, Nagoya Women's University, 3-40 Shioji-cho, Mizuho-ku, Nagoya, Aichi 467-8610, Japan
| | - Tamio Ohno
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan.
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18
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Ebel ER, Uricchio LH, Petrov DA, Egan ES. Revisiting the malaria hypothesis: accounting for polygenicity and pleiotropy. Trends Parasitol 2022; 38:290-301. [PMID: 35065882 PMCID: PMC8916997 DOI: 10.1016/j.pt.2021.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 10/19/2022]
Abstract
The malaria hypothesis predicts local, balancing selection of deleterious alleles that confer strong protection from malaria. Three protective variants, recently discovered in red cell genes, are indeed more common in African than European populations. Still, up to 89% of the heritability of severe malaria is attributed to many genome-wide loci with individually small effects. Recent analyses of hundreds of genome-wide association studies (GWAS) in humans suggest that most functional, polygenic variation is pleiotropic for multiple traits. Interestingly, GWAS alleles and red cell traits associated with small reductions in malaria risk are not enriched in African populations. We propose that other selective and neutral forces, in addition to malaria prevalence, explain the global distribution of most genetic variation impacting malaria risk.
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19
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King R, Lin Z, Balbin-Cuesta G, Myers G, Friedman A, Zhu G, McGee B, Saunders TL, Kurita R, Nakamura Y, Engel JD, Reddy P, Khoriaty R. SEC23A rescues SEC23B-deficient congenital dyserythropoietic anemia type II. SCIENCE ADVANCES 2021; 7:eabj5293. [PMID: 34818036 PMCID: PMC8612686 DOI: 10.1126/sciadv.abj5293] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/04/2021] [Indexed: 05/12/2023]
Abstract
Congenital dyserythropoietic anemia type II (CDAII) results from loss-of-function mutations in SEC23B. In contrast to humans, SEC23B-deficient mice deletion do not exhibit CDAII but die perinatally with pancreatic degeneration. Here, we demonstrate that expression of the full SEC23A protein (the SEC23B paralog) from the endogenous regulatory elements of Sec23b completely rescues the SEC23B-deficient mouse phenotype. Consistent with these data, while mice with erythroid-specific deletion of either Sec23a or Sec23b do not exhibit CDAII, we now show that mice with erythroid-specific deletion of all four Sec23 alleles die in mid-embryogenesis with features of CDAII and that mice with deletion of three Sec23 alleles exhibit a milder erythroid defect. To test whether the functional overlap between the SEC23 paralogs is conserved in human erythroid cells, we generated SEC23B-deficient HUDEP-2 cells. Upon differentiation, these cells exhibited features of CDAII, which were rescued by increased expression of SEC23A, suggesting a novel therapeutic strategy for CDAII.
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Affiliation(s)
- Richard King
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Zesen Lin
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
| | - Ginette Balbin-Cuesta
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA
| | - Gregg Myers
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ann Friedman
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Guojing Zhu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Beth McGee
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Thomas L. Saunders
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI, USA
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Ibaraki, Japan
| | - James Douglas Engel
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Pavan Reddy
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Rami Khoriaty
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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20
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Ebel ER, Kuypers FA, Lin C, Petrov DA, Egan ES. Common host variation drives malaria parasite fitness in healthy human red cells. eLife 2021; 10:e69808. [PMID: 34553687 PMCID: PMC8497061 DOI: 10.7554/elife.69808] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/22/2021] [Indexed: 12/11/2022] Open
Abstract
The replication of Plasmodium falciparum parasites within red blood cells (RBCs) causes severe disease in humans, especially in Africa. Deleterious alleles like hemoglobin S are well-known to confer strong resistance to malaria, but the effects of common RBC variation are largely undetermined. Here, we collected fresh blood samples from 121 healthy donors, most with African ancestry, and performed exome sequencing, detailed RBC phenotyping, and parasite fitness assays. Over one-third of healthy donors unknowingly carried alleles for G6PD deficiency or hemoglobinopathies, which were associated with characteristic RBC phenotypes. Among non-carriers alone, variation in RBC hydration, membrane deformability, and volume was strongly associated with P. falciparum growth rate. Common genetic variants in PIEZO1, SPTA1/SPTB, and several P. falciparum invasion receptors were also associated with parasite growth rate. Interestingly, we observed little or negative evidence for divergent selection on non-pathogenic RBC variation between Africans and Europeans. These findings suggest a model in which globally widespread variation in a moderate number of genes and phenotypes modulates P. falciparum fitness in RBCs.
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Affiliation(s)
- Emily R Ebel
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Pediatrics, Stanford University School of MedicineStanfordUnited States
| | - Frans A Kuypers
- Children's Hospital Oakland Research InstituteOaklandUnited States
| | - Carrie Lin
- Department of Pediatrics, Stanford University School of MedicineStanfordUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Elizabeth S Egan
- Department of Pediatrics, Stanford University School of MedicineStanfordUnited States
- Department of Microbiology & Immunology, Stanford University School of MedicineStanfordUnited States
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21
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Mózner O, Zámbó B, Sarkadi B. Modulation of the Human Erythroid Plasma Membrane Calcium Pump (PMCA4b) Expression by Polymorphic Genetic Variants. MEMBRANES 2021; 11:membranes11080586. [PMID: 34436349 PMCID: PMC8401972 DOI: 10.3390/membranes11080586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 01/10/2023]
Abstract
In the human ATP2B4 gene, coding for the plasma membrane calcium pump PMCA4b, a minor haplotype results in the decreased expression of this membrane protein in erythroid cells. The presence of this haplotype and the consequently reduced PMCA4b expression have been suggested to affect red blood cell hydration and malaria susceptibility. By using dual-luciferase reporter assays, we have localized the erythroid-specific regulatory region within the haplotype of the ATP2B4 gene, containing predicted GATA1 binding sites that are affected by SNPs in the minor haplotype. Our results show that, in human erythroid cells, the regulation of ATP2B4 gene expression is significantly affected by GATA1 expression, and we document the role of specific SNPs involved in predicted GATA1 binding. Our findings provide a mechanistic explanation at the molecular level for the reduced erythroid-specific PMCA4b expression in carriers of ATP2B4 gene polymorphic variants.
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Affiliation(s)
- Orsolya Mózner
- Research Centre for Natural Sciences, Institute of Enzymology, ELKH, 1117 Budapest, Hungary; (O.M.); (B.Z.)
- Doctoral School of Molecular Medicine, Semmelweis University, 1094 Budapest, Hungary
| | - Boglárka Zámbó
- Research Centre for Natural Sciences, Institute of Enzymology, ELKH, 1117 Budapest, Hungary; (O.M.); (B.Z.)
| | - Balázs Sarkadi
- Research Centre for Natural Sciences, Institute of Enzymology, ELKH, 1117 Budapest, Hungary; (O.M.); (B.Z.)
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary
- Correspondence:
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22
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Villegas-Mendez A, Stafford N, Haley MJ, Pravitasari NE, Baudoin F, Ali A, Asih PBS, Siregar JE, Baena E, Syafruddin D, Couper KN, Oceandy D. The plasma membrane calcium ATPase 4 does not influence parasite levels but partially promotes experimental cerebral malaria during murine blood stage malaria. Malar J 2021; 20:297. [PMID: 34215257 PMCID: PMC8252299 DOI: 10.1186/s12936-021-03832-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/24/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Recent genome wide analysis studies have identified a strong association between single nucleotide variations within the human ATP2B4 gene and susceptibility to severe malaria. The ATP2B4 gene encodes the plasma membrane calcium ATPase 4 (PMCA4), which is responsible for controlling the physiological level of intracellular calcium in many cell types, including red blood cells (RBCs). It is, therefore, postulated that genetic differences in the activity or expression level of PMCA4 alters intracellular Ca2+ levels and affects RBC hydration, modulating the invasion and growth of the Plasmodium parasite within its target host cell. METHODS In this study the course of three different Plasmodium spp. infections were examined in mice with systemic knockout of Pmca4 expression. RESULTS Ablation of PMCA4 reduced the size of RBCs and their haemoglobin content but did not affect RBC maturation and reticulocyte count. Surprisingly, knockout of PMCA4 did not significantly alter peripheral parasite burdens or the dynamics of blood stage Plasmodium chabaudi infection or reticulocyte-restricted Plasmodium yoelii infection. Interestingly, although ablation of PMCA4 did not affect peripheral parasite levels during Plasmodium berghei infection, it did promote slight protection against experimental cerebral malaria, associated with a minor reduction in antigen-experienced T cell accumulation in the brain. CONCLUSIONS The finding suggests that PMCA4 may play a minor role in the development of severe malarial complications, but that this appears independent of direct effects on parasite invasion, growth or survival within RBCs.
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Affiliation(s)
- Ana Villegas-Mendez
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Nicholas Stafford
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Michael J Haley
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | | | - Florence Baudoin
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Adnan Ali
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Manchester, SK10 4TG, UK
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
| | | | | | - Esther Baena
- Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Manchester, SK10 4TG, UK
| | - Din Syafruddin
- Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia
| | - Kevin N Couper
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK.
| | - Delvac Oceandy
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK.
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23
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Bagchi A, Nath A, Thamodaran V, Ijee S, Palani D, Rajendiran V, Venkatesan V, Datari P, Pai AA, Janet NB, Balasubramanian P, Nakamura Y, Srivastava A, Mohankumar KM, Thangavel S, Velayudhan SR. Direct Generation of Immortalized Erythroid Progenitor Cell Lines from Peripheral Blood Mononuclear Cells. Cells 2021; 10:523. [PMID: 33804564 PMCID: PMC7999632 DOI: 10.3390/cells10030523] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/08/2021] [Accepted: 02/19/2021] [Indexed: 02/04/2023] Open
Abstract
Reliable human erythroid progenitor cell (EPC) lines that can differentiate to the later stages of erythropoiesis are important cellular models for studying molecular mechanisms of human erythropoiesis in normal and pathological conditions. Two immortalized erythroid progenitor cells (iEPCs), HUDEP-2 and BEL-A, generated from CD34+ hematopoietic progenitors by the doxycycline (dox) inducible expression of human papillomavirus E6 and E7 (HEE) genes, are currently being used extensively to study transcriptional regulation of human erythropoiesis and identify novel therapeutic targets for red cell diseases. However, the generation of iEPCs from patients with red cell diseases is challenging as obtaining a sufficient number of CD34+ cells require bone marrow aspiration or their mobilization to peripheral blood using drugs. This study established a protocol for culturing early-stage EPCs from peripheral blood (PB) and their immortalization by expressing HEE genes. We generated two iEPCs, PBiEPC-1 and PBiEPC-2, from the peripheral blood mononuclear cells (PBMNCs) of two healthy donors. These cell lines showed stable doubling times with the properties of erythroid progenitors. PBiEPC-1 showed robust terminal differentiation with high enucleation efficiency, and it could be successfully gene manipulated by gene knockdown and knockout strategies with high efficiencies without affecting its differentiation. This protocol is suitable for generating a bank of iEPCs from patients with rare red cell genetic disorders for studying disease mechanisms and drug discovery.
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Affiliation(s)
- Abhirup Bagchi
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Aneesha Nath
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Vasanth Thamodaran
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Smitha Ijee
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Dhavapriya Palani
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Vignesh Rajendiran
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Vigneshwaran Venkatesan
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Phaneendra Datari
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
| | - Aswin Anand Pai
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
| | - Nancy Beryl Janet
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
| | - Poonkuzhali Balasubramanian
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Ibaraki 3050074, Japan;
| | - Alok Srivastava
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
| | - Kumarasamypet Murugesan Mohankumar
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Saravanabhavan Thangavel
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
| | - Shaji R. Velayudhan
- Center for Stem Cell Research (A Unit of InStem, Bengaluru, India), Christian Medical College, Vellore 632002, Tamil Nadu, India; (A.B.); (A.N.); (V.T.); (S.I.); (D.P.); (V.R.); (V.V.); (A.S.); (K.M.M.); (S.T.)
- Department of Hematology, Christian Medical College, Vellore 632002, Tamil Nadu, India; (P.D.); (A.A.P.); (N.B.J.); (P.B.)
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Nwokocha CR, Bafor EE, Ajayi OI, Ebeigbe AB. The Malaria-High Blood Pressure Hypothesis: Revisited. Am J Hypertens 2020; 33:695-702. [PMID: 32211753 DOI: 10.1093/ajh/hpaa051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 02/24/2020] [Accepted: 03/18/2020] [Indexed: 11/14/2022] Open
Abstract
Malaria etiologies with pathophysiological similarities to hypertension currently constitute a major subject of research. The malaria-high blood pressure hypothesis is strongly supported by observations of the increasing incidence of hypertension in malaria-endemic, low- and middle-income countries with poor socioeconomic conditions, particularly in sub-Saharan African countries. Malnutrition and low birth weight with persistent symptomatic malaria presentations in pregnancy correlate strongly with the development of preeclampsia, gestational hypertension and subsequent hypertension in adult life. Evidence suggest that the link between malaria infection and high blood pressure involves interactions between malaria parasites and erythrocytes, the inflammatory process, effects of the infection during pregnancy; effects on renal and vascular functions as well as effects in sickle cell disease. Possible mechanisms which provide justification for the malaria-high blood pressure hypothesis include the following: endothelial dysfunction (reduced nitric oxide (NO) levels), impaired release of local neurotransmitters and cytokines, decrease in vascular smooth muscle cell viability and/or alterations in cellular calcium signaling leading to enhanced vascular reactivity, remodeling, and cardiomyopathies, deranged homeostasis through dehydration, elevated intracellular mediators and proinflammatory cytokine responses, possible genetic regulations, activation of the renin-angiotensin-aldosterone system mechanisms and renal derangements, severe anemia and hemolysis, renal failure, and end organ damage. Two key mediators of the malaria-high blood pressure association are: endothelial dysfunction (reduced NO) and increased angiotensin-converting enzyme activity/angiotensin II levels. Sickle cell disease is associated with protection against malaria infection and reduced blood pressure. In this review, we present the state of knowledge about the malaria-blood pressure hypothesis and suggest insights for future studies.
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Affiliation(s)
| | - Enitome E Bafor
- Department of Pharmacology and Toxicology, University of Benin, Benin City, Nigeria
| | - Olutayo I Ajayi
- Department of Physiology, College of Medical Sciences, University of Benin, Benin City, Nigeria
| | - Anthony B Ebeigbe
- Department of Physiology, College of Medical Sciences, University of Benin, Benin City, Nigeria
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25
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Abstract
Malaria has been the pre-eminent cause of early mortality in many parts of the world throughout much of the last five thousand years and, as a result, it is the strongest force for selective pressure on the human genome yet described. Around one third of the variability in the risk of severe and complicated malaria is now explained by additive host genetic effects. Many individual variants have been identified that are associated with malaria protection, but the most important all relate to the structure or function of red blood cells. They include the classical polymorphisms that cause sickle cell trait, α-thalassaemia, G6PD deficiency, and the major red cell blood group variants. More recently however, with improving technology and experimental design, others have been identified that include the Dantu blood group variant, polymorphisms in the red cell membrane protein ATP2B4, and several variants related to the immune response. Characterising how these genes confer their effects could eventually inform novel therapeutic approaches to combat malaria. Nevertheless, all together, only a small proportion of the heritable component of malaria resistance can be explained by the variants described so far, underscoring its complex genetic architecture and the need for continued research.
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Affiliation(s)
- Silvia N Kariuki
- Department of Epidemiology, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
| | - Thomas N Williams
- Department of Epidemiology, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
- Department of Medicine, Imperial College of Science and Technology, London, UK.
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26
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Chen J, Sitsel A, Benoy V, Sepúlveda MR, Vangheluwe P. Primary Active Ca 2+ Transport Systems in Health and Disease. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035113. [PMID: 31501194 DOI: 10.1101/cshperspect.a035113] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Calcium ions (Ca2+) are prominent cell signaling effectors that regulate a wide variety of cellular processes. Among the different players in Ca2+ homeostasis, primary active Ca2+ transporters are responsible for keeping low basal Ca2+ levels in the cytosol while establishing steep Ca2+ gradients across intracellular membranes or the plasma membrane. This review summarizes our current knowledge on the three types of primary active Ca2+-ATPases: the sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA) pumps, the secretory pathway Ca2+- ATPase (SPCA) isoforms, and the plasma membrane Ca2+-ATPase (PMCA) Ca2+-transporters. We first discuss the Ca2+ transport mechanism of SERCA1a, which serves as a reference to describe the Ca2+ transport of other Ca2+ pumps. We further highlight the common and unique features of each isoform and review their structure-function relationship, expression pattern, regulatory mechanisms, and specific physiological roles. Finally, we discuss the increasing genetic and in vivo evidence that links the dysfunction of specific Ca2+-ATPase isoforms to a broad range of human pathologies, and highlight emerging therapeutic strategies that target Ca2+ pumps.
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Affiliation(s)
- Jialin Chen
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Aljona Sitsel
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Veronick Benoy
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - M Rosario Sepúlveda
- Department of Cell Biology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Peter Vangheluwe
- Laboratory of Cellular Transport Systems, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
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27
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Hegedűs L, Zámbó B, Pászty K, Padányi R, Varga K, Penniston JT, Enyedi Á. Molecular Diversity of Plasma Membrane Ca2+ Transporting ATPases: Their Function Under Normal and Pathological Conditions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1131:93-129. [DOI: 10.1007/978-3-030-12457-1_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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28
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Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania. Nat Commun 2019; 10:5732. [PMID: 31844061 PMCID: PMC6914791 DOI: 10.1038/s41467-019-13480-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 11/11/2019] [Indexed: 12/31/2022] Open
Abstract
The human genetic factors that affect resistance to infectious disease are poorly understood. Here we report a genome-wide association study in 17,000 severe malaria cases and population controls from 11 countries, informed by sequencing of family trios and by direct typing of candidate loci in an additional 15,000 samples. We identify five replicable associations with genome-wide levels of evidence including a newly implicated variant on chromosome 6. Jointly, these variants account for around one-tenth of the heritability of severe malaria, which we estimate as ~23% using genome-wide genotypes. We interrogate available functional data and discover an erythroid-specific transcription start site underlying the known association in ATP2B4, but are unable to identify a likely causal mechanism at the chromosome 6 locus. Previously reported HLA associations do not replicate in these samples. This large dataset will provide a foundation for further research on the genetic determinants of malaria resistance in diverse populations. Four genome-wide associated loci are currently known for malaria susceptibility. Here, the authors expand on earlier work by combining data from 11 malaria-endemic countries and additional population sequencing informing an African-enriched imputation reference panel, with findings including a previously unreported association on chromosome 6.
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29
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Damena D, Denis A, Golassa L, Chimusa ER. Genome-wide association studies of severe P. falciparum malaria susceptibility: progress, pitfalls and prospects. BMC Med Genomics 2019; 12:120. [PMID: 31409341 PMCID: PMC6693204 DOI: 10.1186/s12920-019-0564-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 07/29/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND P. falciparum malaria has been recognized as one of the prominent evolutionary selective forces of human genome that led to the emergence of multiple host protective alleles. A comprehensive understanding of the genetic bases of severe malaria susceptibility and resistance can potentially pave ways to the development of new therapeutics and vaccines. Genome-wide association studies (GWASs) have recently been implemented in malaria endemic areas and identified a number of novel association genetic variants. However, there are several open questions around heritability, epistatic interactions, genetic correlations and associated molecular pathways among others. Here, we assess the progress and pitfalls of severe malaria susceptibility GWASs and discuss the biology of the novel variants. RESULTS We obtained all severe malaria susceptibility GWASs published thus far and accessed GWAS dataset of Gambian populations from European Phenome Genome Archive (EGA) through the MalariaGen consortium standard data access protocols. We noticed that, while some of the well-known variants including HbS and ABO blood group were replicated across endemic populations, only few novel variants were convincingly identified and their biological functions remain to be understood. We estimated SNP-heritability of severe malaria at 20.1% in Gambian populations and showed how advanced statistical genetic analytic methods can potentially be implemented in malaria susceptibility studies to provide useful functional insights. CONCLUSIONS The ultimate goal of malaria susceptibility study is to discover a novel causal biological pathway that provide protections against severe malaria; a fundamental step towards translational medicine such as development of vaccine and new therapeutics. Beyond singe locus analysis, the future direction of malaria susceptibility requires a paradigm shift from single -omics to multi-stage and multi-dimensional integrative functional studies that combines multiple data types from the human host, the parasite, the mosquitoes and the environment. The current biotechnological and statistical advances may eventually lead to the feasibility of systems biology studies and revolutionize malaria research.
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Affiliation(s)
- Delesa Damena
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7700 South Africa
| | - Awany Denis
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7700 South Africa
| | - Lemu Golassa
- Aklilu Lema Institute of Pathobiology, Addis Ababa University, PO box 1176, Addis Ababa, Ethiopia
| | - Emile R. Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7700 South Africa
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30
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Lalonde S, Codina-Fauteux VA, de Bellefon SM, Leblanc F, Beaudoin M, Simon MM, Dali R, Kwan T, Lo KS, Pastinen T, Lettre G. Integrative analysis of vascular endothelial cell genomic features identifies AIDA as a coronary artery disease candidate gene. Genome Biol 2019; 20:133. [PMID: 31287004 PMCID: PMC6613242 DOI: 10.1186/s13059-019-1749-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 06/27/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified hundreds of loci associated with coronary artery disease (CAD) and blood pressure (BP) or hypertension. Many of these loci are not linked to traditional risk factors, nor do they include obvious candidate genes, complicating their functional characterization. We hypothesize that many GWAS loci associated with vascular diseases modulate endothelial functions. Endothelial cells play critical roles in regulating vascular homeostasis, such as roles in forming a selective barrier, inflammation, hemostasis, and vascular tone, and endothelial dysfunction is a hallmark of atherosclerosis and hypertension. To test this hypothesis, we generate an integrated map of gene expression, open chromatin region, and 3D interactions in resting and TNFα-treated human endothelial cells. RESULTS We show that genetic variants associated with CAD and BP are enriched in open chromatin regions identified in endothelial cells. We identify physical loops by Hi-C and link open chromatin peaks that include CAD or BP SNPs with the promoters of genes expressed in endothelial cells. This analysis highlights 991 combinations of open chromatin regions and gene promoters that map to 38 CAD and 92 BP GWAS loci. We validate one CAD locus, by engineering a deletion of the TNFα-sensitive regulatory element using CRISPR/Cas9 and measure the effect on the expression of the novel CAD candidate gene AIDA. CONCLUSIONS Our data support an important role played by genetic variants acting in the vascular endothelium to modulate inter-individual risk in CAD and hypertension.
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Affiliation(s)
- Simon Lalonde
- Montreal Heart Institute, 5000 Belanger street, Montréal, Québec H1T 1C8 Canada
| | - Valérie-Anne Codina-Fauteux
- Montreal Heart Institute, 5000 Belanger street, Montréal, Québec H1T 1C8 Canada
- Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4 Canada
| | - Sébastian Méric de Bellefon
- Montreal Heart Institute, 5000 Belanger street, Montréal, Québec H1T 1C8 Canada
- Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4 Canada
| | - Francis Leblanc
- Montreal Heart Institute, 5000 Belanger street, Montréal, Québec H1T 1C8 Canada
- Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4 Canada
| | - Mélissa Beaudoin
- Montreal Heart Institute, 5000 Belanger street, Montréal, Québec H1T 1C8 Canada
| | - Marie-Michelle Simon
- McGill University and Genome Québec Innovation Center, Montréal, Québec H3A 0G1 Canada
| | - Rola Dali
- McGill University and Genome Québec Innovation Center, Montréal, Québec H3A 0G1 Canada
| | - Tony Kwan
- McGill University and Genome Québec Innovation Center, Montréal, Québec H3A 0G1 Canada
| | - Ken Sin Lo
- Montreal Heart Institute, 5000 Belanger street, Montréal, Québec H1T 1C8 Canada
| | - Tomi Pastinen
- Center for Pediatric Genomic Medicine (CPGM), Children’s Mercy Kansas City, 2401 Gillham Road, Kansas City, MO 64108 USA
| | - Guillaume Lettre
- Montreal Heart Institute, 5000 Belanger street, Montréal, Québec H1T 1C8 Canada
- Faculté de Médecine, Université de Montréal, Montréal, Québec H3T 1J4 Canada
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31
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Ohno T, Miyasaka Y, Kuga M, Ushida K, Matsushima M, Kawabe T, Kikkawa Y, Mizuno M, Takahashi M. Mouse NC/Jic strain provides novel insights into host genetic factors for malaria research. Exp Anim 2019; 68:243-255. [PMID: 30880305 PMCID: PMC6699971 DOI: 10.1538/expanim.18-0185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Malaria is caused by Plasmodium parasites and is one of the most
life-threatening infectious diseases in humans. Infection can result in severe
complications such as cerebral malaria, acute lung injury/acute respiratory distress
syndrome, and acute renal injury. These complications are mainly caused by P.
falciparum infection and are major causes of death associated with malaria.
There are a few species of rodent-infective malaria parasites, and mice infected with such
parasites are now widely used for screening candidate drugs and vaccines and for studying
host immune responses and pathogenesis associated with disease-related complications. We
found that mice of the NC/Jic strain infected with rodent malarial parasites exhibit
distinctive disease-related complications such as cerebral malaria and nephrotic syndrome,
in addition to a rapid increase in parasitemia. Here, we focus on the analysis of host
genetic factors that affect malarial pathogenesis and describe the characteristic
features, utility, and future prospects for exploitation of the NC/Jic strain as a novel
mouse model for malaria research.
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Affiliation(s)
- Tamio Ohno
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Yuki Miyasaka
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Masako Kuga
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Kaori Ushida
- Department of Pathology, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Miyoko Matsushima
- Department of Pathophysiological Laboratory Sciences, Graduate School of Medicine, Nagoya University, 1-1-20 Daikou-minami, Higashi-ku, Nagoya, Aichi 461-8673, Japan
| | - Tsutomu Kawabe
- Department of Pathophysiological Laboratory Sciences, Graduate School of Medicine, Nagoya University, 1-1-20 Daikou-minami, Higashi-ku, Nagoya, Aichi 461-8673, Japan
| | - Yoshiaki Kikkawa
- Mammalian Genetics Project, Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Masashi Mizuno
- Renal Replacement Therapy, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Masahide Takahashi
- Department of Pathology, Graduate School of Medicine, Nagoya University, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
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32
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Gouveia MH, Bergen AW, Borda V, Nunes K, Leal TP, Ogwang MD, Yeboah ED, Mensah JE, Kinyera T, Otim I, Nabalende H, Legason ID, Mpoloka SW, Mokone GG, Kerchan P, Bhatia K, Reynolds SJ, Birtwum RB, Adjei AA, Tettey Y, Tay E, Hoover R, Pfeiffer RM, Biggar RJ, Goedert JJ, Prokunina-Olsson L, Dean M, Yeager M, Lima-Costa MF, Hsing AW, Tishkoff SA, Chanock SJ, Tarazona-Santos E, Mbulaiteye SM. Genetic signatures of gene flow and malaria-driven natural selection in sub-Saharan populations of the "endemic Burkitt Lymphoma belt". PLoS Genet 2019; 15:e1008027. [PMID: 30849090 PMCID: PMC6426263 DOI: 10.1371/journal.pgen.1008027] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 03/20/2019] [Accepted: 02/17/2019] [Indexed: 12/13/2022] Open
Abstract
Populations in sub-Saharan Africa have historically been exposed to intense selection from chronic infection with falciparum malaria. Interestingly, populations with the highest malaria intensity can be identified by the increased occurrence of endemic Burkitt Lymphoma (eBL), a pediatric cancer that affects populations with intense malaria exposure, in the so called "eBL belt" in sub-Saharan Africa. However, the effects of intense malaria exposure and sub-Saharan populations' genetic histories remain poorly explored. To determine if historical migrations and intense malaria exposure have shaped the genetic composition of the eBL belt populations, we genotyped ~4.3 million SNPs in 1,708 individuals from Ghana and Northern Uganda, located on opposite sides of eBL belt and with ≥ 7 months/year of intense malaria exposure and published evidence of high incidence of BL. Among 35 Ghanaian tribes, we showed a predominantly West-Central African ancestry and genomic footprints of gene flow from Gambian and East African populations. In Uganda, the North West population showed a predominantly Nilotic ancestry, and the North Central population was a mixture of Nilotic and Southern Bantu ancestry, while the Southwest Ugandan population showed a predominant Southern Bantu ancestry. Our results support the hypothesis of diverse ancestral origins of the Ugandan, Kenyan and Tanzanian Great Lakes African populations, reflecting a confluence of Nilotic, Cushitic and Bantu migrations in the last 3000 years. Natural selection analyses suggest, for the first time, a strong positive selection signal in the ATP2B4 gene (rs10900588) in Northern Ugandan populations. These findings provide important baseline genomic data to facilitate disease association studies, including of eBL, in eBL belt populations.
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Affiliation(s)
- Mateus H. Gouveia
- Instituto de Pesquisa René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Center for Research on Genomics & Global Health, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Andrew W. Bergen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Victor Borda
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Kelly Nunes
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Thiago P. Leal
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Statistics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Martin D. Ogwang
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | | | | | - Tobias Kinyera
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Isaac Otim
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | | | | | | | - Gaonyadiwe George Mokone
- Department of Biomedical Sciences, University of Botswana School of Medicine, Gaborone, Botswana
| | - Patrick Kerchan
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Kishor Bhatia
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Steven J. Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | | | | | - Yao Tettey
- University of Ghana Medical School, Accra, Ghana
| | - Evelyn Tay
- University of Ghana Medical School, Accra, Ghana
| | - Robert Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Ruth M. Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Robert J. Biggar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - James J. Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, US Department of Health and Human Services, Frederick, Maryland, United States of America
| | - M. Fernanda Lima-Costa
- Instituto de Pesquisa René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Ann W. Hsing
- Stanford Cancer Institute, Stanford University, Stanford, California, United States of America
| | - Sarah A. Tishkoff
- Department of Genetics and Biology, University of Pennsylvania, Philadelphia, United States of America
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Eduardo Tarazona-Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sam M. Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, United States of America
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33
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Lessard S, Beaudoin M, Orkin SH, Bauer DE, Lettre G. 14q32 and let-7 microRNAs regulate transcriptional networks in fetal and adult human erythroblasts. Hum Mol Genet 2019; 27:1411-1420. [PMID: 29432581 DOI: 10.1093/hmg/ddy051] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/05/2018] [Indexed: 12/29/2022] Open
Abstract
In humans, fetal erythropoiesis takes place in the liver whereas adult erythropoiesis occurs in the bone marrow. Fetal and adult erythroid cells are not only produced at different sites, but are also distinguished by their respective transcriptional program. In particular, whereas fetal erythroid cells express γ-globin chains to produce fetal hemoglobin (HbF), adult cells express β-globin chains to generate adult hemoglobin. Understanding the transcriptional regulation of the fetal-to-adult hemoglobin switch is clinically important as re-activation of HbF production in adult erythroid cells would represent a promising therapy for the hemoglobin disorders sickle cell disease and β-thalassemia. We used RNA-sequencing to measure global gene and microRNA (miRNA) expression in human erythroblasts derived ex vivo from fetal liver (n = 12 donors) and bone marrow (n = 12 donors) hematopoietic stem/progenitor cells. We identified 7829 transcripts and 402 miRNA that were differentially expressed (false discovery rate <5%). The miRNA expression patterns were replicated in an independent collection of human erythroblasts using a different technology. By combining gene and miRNA expression data, we developed transcriptional networks which show substantial differences between fetal and adult human erythroblasts. Our analyses highlighted the miRNAs at the imprinted 14q32 locus in fetal erythroblasts and the let-7 miRNA family in adult erythroblasts as key regulators of stage-specific erythroid transcriptional programs. Altogether, our results provide a comprehensive resource to prioritize genes that may modify clinical severity in red blood cell (RBC) disorders, or genes that might be implicated in erythropoiesis by genome-wide association studies of RBC traits.
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Affiliation(s)
- Samuel Lessard
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada.,Faculté de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | | | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada.,Faculté de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
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34
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Ilboudo Y, Bartolucci P, Garrett ME, Ashley-Koch A, Telen M, Brugnara C, Galactéros F, Lettre G. A common functional PIEZO1 deletion allele associates with red blood cell density in sickle cell disease patients. Am J Hematol 2018; 93:E362-E365. [PMID: 30105803 DOI: 10.1002/ajh.25245] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/06/2018] [Indexed: 01/25/2023]
Affiliation(s)
- Yann Ilboudo
- Faculty of Medicine; Université de Montréal; Montreal Quebec Canada
- Montreal Heart Institute; Montreal Quebec Canada
| | - Pablo Bartolucci
- Red Cell Genetic Disease Unit; Hôpital Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP); Créteil France
| | - Melanie E. Garrett
- Center for Human Disease Modeling; Duke University Medical Center; Durham North Carolina
- Department of Medicine, Division of Hematology; Duke University Medical Center; Durham North Carolina
| | - Allison Ashley-Koch
- Center for Human Disease Modeling; Duke University Medical Center; Durham North Carolina
- Department of Medicine, Division of Hematology; Duke University Medical Center; Durham North Carolina
| | - Marilyn Telen
- Center for Human Disease Modeling; Duke University Medical Center; Durham North Carolina
- Department of Medicine, Division of Hematology; Duke University Medical Center; Durham North Carolina
| | - Carlo Brugnara
- Department of Laboratory Medicine; Boston Children's Hospital; Boston Massachusetts
| | - Frédéric Galactéros
- Red Cell Genetic Disease Unit; Hôpital Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP); Créteil France
| | - Guillaume Lettre
- Faculty of Medicine; Université de Montréal; Montreal Quebec Canada
- Montreal Heart Institute; Montreal Quebec Canada
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Arama C, Quin JE, Kouriba B, Östlund Farrants AK, Troye-Blomberg M, Doumbo OK. Epigenetics and Malaria Susceptibility/Protection: A Missing Piece of the Puzzle. Front Immunol 2018; 9:1733. [PMID: 30158923 PMCID: PMC6104485 DOI: 10.3389/fimmu.2018.01733] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/12/2018] [Indexed: 12/22/2022] Open
Abstract
A better understanding of stable changes in regulation of gene expression that result from epigenetic events is of great relevance in the development of strategies to prevent and treat infectious diseases. Histone modification and DNA methylation are key epigenetic mechanisms that can be regarded as marks, which ensure an accurate transmission of the chromatin states and gene expression profiles over generations of cells. There is an increasing list of these modifications, and the complexity of their action is just beginning to be understood. It is clear that the epigenetic landscape plays a fundamental role in most biological processes that involve the manipulation and expression of DNA. Although the molecular mechanism of gene regulation is relatively well understood, the hierarchical order of events and dependencies that lead to protection against infection remain largely unknown. In this review, we propose that host epigenetics is an essential, though relatively under studied, factor in the protection or susceptibility to malaria.
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Affiliation(s)
- Charles Arama
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Jaclyn E Quin
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Bourèma Kouriba
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | | | - Marita Troye-Blomberg
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Ogobara K Doumbo
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
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36
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Moir-Meyer G, Cheong PL, Olijnik AA, Brown J, Knight S, King A, Kurita R, Nakamura Y, Gibbons RJ, Higgs DR, Buckle VJ, Babbs C. Robust CRISPR/Cas9 Genome Editing of the HUDEP-2 Erythroid Precursor Line Using Plasmids and Single-Stranded Oligonucleotide Donors. Methods Protoc 2018; 1:E28. [PMID: 31164570 PMCID: PMC6481050 DOI: 10.3390/mps1030028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/13/2018] [Accepted: 07/23/2018] [Indexed: 12/23/2022] Open
Abstract
The study of cellular processes and gene regulation in terminal erythroid development has been greatly facilitated by the generation of an immortalised erythroid cell line derived from Human Umbilical Derived Erythroid Precursors, termed HUDEP-2 cells. The ability to efficiently genome edit HUDEP-2 cells and make clonal lines hugely expands their utility as the insertion of clinically relevant mutations allows study of potentially every genetic disease affecting red blood cell development. Additionally, insertion of sequences encoding short protein tags such as Strep, FLAG and Myc permits study of protein behaviour in the normal and disease state. This approach is useful to augment the analysis of patient cells as large cell numbers are obtainable with the additional benefit that the need for specific antibodies may be circumvented. This approach is likely to lead to insights into disease mechanisms and provide reagents to allow drug discovery. HUDEP-2 cells provide a favourable alternative to the existing immortalised erythroleukemia lines as their karyotype is much less abnormal. These cells also provide sufficient material for a broad range of analyses as it is possible to generate in vitro-differentiated erythroblasts in numbers 4-7 fold higher than starting cell numbers within 9-12 days of culture. Here we describe an efficient, robust and reproducible plasmid-based methodology to introduce short (<20 bp) DNA sequences into the genome of HUDEP-2 cells using the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 Cas9 system combined with single-stranded oligodeoxynucleotide (ssODN) donors. This protocol produces genetically modified lines in ~30 days and could also be used to generate knock-out and knock-in mutations.
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Affiliation(s)
- Gemma Moir-Meyer
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Pak Leng Cheong
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Aude-Anais Olijnik
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Jill Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Samantha Knight
- Wellcome Trust Centre for Human Genetics, Oxford University, Oxford OX3 7BN, UK.
| | - Andrew King
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Japanese Red Cross Society, 1-1-3 Shibadaimon, Minato-ku, Tokyo 105-8521, Japan.
| | - Yukio Nakamura
- RIKEN BioResource Research Center, Koyadai 3-1-1, Tsukuba 305-0074, Japan.
| | - Richard J Gibbons
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Christian Babbs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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CRISPR-based strategies for studying regulatory elements and chromatin structure in mammalian gene control. Mamm Genome 2018; 29:205-228. [PMID: 29196861 PMCID: PMC9881389 DOI: 10.1007/s00335-017-9727-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/27/2017] [Indexed: 01/31/2023]
Abstract
The development of high-throughput methods has enabled the genome-wide identification of putative regulatory elements in a wide variety of mammalian cells at an unprecedented resolution. Extensive genomic studies have revealed the important role of regulatory elements and genetic variation therein in disease formation and risk. In most cases, there is only correlative evidence for the roles of these elements and non-coding changes within these elements in pathogenesis. With the advent of genome- and epigenome-editing tools based on the CRISPR technology, it is now possible to test the functional relevance of the regulatory elements and alterations on a genomic scale. Here, we review the various CRISPR-based strategies that have been developed to functionally validate the candidate regulatory elements in mammals as well as the non-coding genetic variants found to be associated with human disease. We also discuss how these synthetic biology tools have helped to elucidate the role of three-dimensional nuclear architecture and higher-order chromatin organization in shaping functional genome and controlling gene expression.
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38
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Huang HM, McMorran BJ, Foote SJ, Burgio G. Host genetics in malaria: lessons from mouse studies. Mamm Genome 2018; 29:507-522. [PMID: 29594458 DOI: 10.1007/s00335-018-9744-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 03/22/2018] [Indexed: 01/09/2023]
Abstract
Malaria remains a deadly parasitic disease caused by Plasmodium, claiming almost half a million lives every year. While parasite genetics and biology are often the major targets in many studies, it is becoming more evident that host genetics plays a crucial role in the outcome of the infection. Similarly, Plasmodium infections in mice also rely heavily on the genetic background of the mice, and often correlate with observations in human studies, due to their high genetic homology with humans. As such, murine models of malaria are a useful tool for understanding host responses during Plasmodium infections, as well as dissecting host-parasite interactions through various genetic manipulation techniques. Reverse genetic approach such as quantitative trait loci studies and random mutagenesis screens have been employed to discover novel host genes that affect malaria susceptibility in mouse models, while other targeted studies utilize mouse models to validate observation from human studies. Herein, we review the findings from the past and present studies on murine models of hepatic and erythrocytic stages of malaria and speculate on how the current mouse models benefit from the recent development in CRISPR/Cas9 gene editing technology.
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Affiliation(s)
- Hong Ming Huang
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, 131 Garran Road, Canberra, ACT, 2601, Australia
| | - Brendan J McMorran
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, 131 Garran Road, Canberra, ACT, 2601, Australia
| | - Simon J Foote
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, 131 Garran Road, Canberra, ACT, 2601, Australia
| | - Gaetan Burgio
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, 131 Garran Road, Canberra, ACT, 2601, Australia.
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39
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Abstract
The erythrocyte contains a network of pathways that regulate salt and water content in the face of extracellular and intracellular osmotic perturbations. This allows the erythrocyte to maintain a narrow range of cell hemoglobin concentration, a process critical for normal red blood cell function and survival. Primary disorders that perturb volume homeostasis jeopardize the erythrocyte and may lead to its premature destruction. These disorders are marked by clinical, laboratory, and physiologic heterogeneity. Recent studies have revealed that these disorders are also marked by genetic heterogeneity. They have implicated roles for several proteins, PIEZO1, a mammalian mechanosensory protein; GLUT1, the glucose transporter; SLC4A1, the anion transporter; RhAG, the Rh-associated glycoprotein; KCNN4, the Gardos channel; and ABCB6, an adenosine triphosphate-binding cassette family member, in the maintenance of erythrocyte volume homeostasis. Secondary disorders of erythrocyte hydration include sickle cell disease, thalassemia, hemoglobin CC, and hereditary spherocytosis, where cellular dehydration may be a significant contributor to disease pathology and clinical complications. Understanding the pathways regulating erythrocyte water and solute content may reveal innovative strategies to maintain normal volume in disorders associated with primary or secondary cellular dehydration. These mechanisms will serve as a paradigm for other cells and may reveal new therapeutic targets for disease prevention and treatment beyond the erythrocyte.
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