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Adjemout M, Gallardo F, Torres M, Thiam A, Mbengue B, Dieye A, Marquet S, Rihet P. From GWAS to functional variants: ARL14 cis-regulatory variants are associated with severe malaria. J Infect Dis 2024:jiae159. [PMID: 38531688 DOI: 10.1093/infdis/jiae159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/05/2024] [Accepted: 03/24/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND GWAS have identified several non-functional tagSNPs 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 IW-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 two 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 Université, INSERM, TAGC, UMR 1090, MarMara Institute, Marseille, France
| | - Frederic Gallardo
- Aix-Marseille Université, INSERM, TAGC, UMR 1090, MarMara Institute, Marseille, France
| | - Magali Torres
- Aix-Marseille Université, INSERM, TAGC, UMR 1090, MarMara Institute, Marseille, France
| | | | - Babacar Mbengue
- Service D'Immunologie, Université Cheikh Anta Diop de Dakar, Dakar BP5005, Sénégal
| | - Alioune Dieye
- Service D'Immunologie, Université Cheikh Anta Diop de Dakar, Dakar BP5005, Sénégal
| | - Sandrine Marquet
- Aix-Marseille Université, INSERM, TAGC, UMR 1090, MarMara Institute, Marseille, France
| | - Pascal Rihet
- Aix-Marseille Université, INSERM, TAGC, UMR 1090, MarMara Institute, Marseille, France
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Madaci L, Gard C, Nin S, Sarrabay A, Baier C, Venton G, Rihet P, Puthier D, Loriod B, Costello R. Single-Cell Transcriptome Analysis of Acute Myeloid Leukemia Cells Using Methanol Fixation and Cryopreservation. Diseases 2023; 12:1. [PMID: 38275564 PMCID: PMC10814800 DOI: 10.3390/diseases12010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
INTRODUCTION The application of single-cell RNA sequencing has greatly improved our understanding of various cellular and molecular mechanisms involved in physiological and pathophysiological processes. However, obtaining living cells for this technique can be difficult under certain conditions. To solve this problem, the methanol fixation method appeared as a promising alternative for routine clinical use. MATERIALS AND METHODS In this study, we selected two AML samples that had been fixed in methanol for 12-18 months. Once the cells were rehydrated, these samples were subjected to single-cell RNA sequencing. We then compared the results obtained from these samples with those obtained from the same samples cryopreserved in DMSO. RESULTS We used a previously validated methanol fixation protocol to perform scRNA-seq on DMSO cryopreserved cells and cells fixed in methanol for more than one year. Preliminary results show that methanol fixation induces some genetic and transcriptional modification compared with DMSO cryopreservation but remains a valuable method for single-cell analysis of primary human leukemia cells. CONCLUSIONS The initial findings from this study highlight certain resemblances in methanol fixation over a 12-month period and cryopreservation with DMSO, along with associated transcriptional level modifications. However, we observed genetic degradation in the fixation condition when extending beyond one year. Despite certain study limitations, it is evident that short-term methanol fixation can be effectively used for leukemia blast samples. Its ease of implementation holds the potential to simplify the integration of this technique into routine clinical practice.
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Affiliation(s)
- Lamia Madaci
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Charlyne Gard
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Sébastien Nin
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Alexandre Sarrabay
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Céline Baier
- Advanced BioDesign, Parc Technologique de Lyon, 655 Allée des Parcs, 69800 Saint Priest, France
| | - Geoffroy Venton
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
| | - Pascal Rihet
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Denis Puthier
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Béatrice Loriod
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
| | - Régis Costello
- TAGC, TGML, INSERM, UMR1090, Aix-Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France; (L.M.); (C.G.); (S.N.); (G.V.); (P.R.); (D.P.); (B.L.)
- Hematology and Cellular Therapy Department, Conception University Hospital, 13005 Marseille, France
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Adjemout M, Pouvelle B, Thiam F, Thiam A, Torres M, Nisar S, Mbengue B, Dieye A, Rihet P, Marquet S. Concurrent PIEZO1 activation and ATP2B4 blockade effectively reduce the risk of cerebral malaria and inhibit in vitro Plasmodium falciparum multiplication in red blood cells. Genes Dis 2023; 10:2210-2214. [PMID: 37554196 PMCID: PMC10404997 DOI: 10.1016/j.gendis.2023.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 02/08/2023] [Indexed: 03/29/2023] Open
Affiliation(s)
- Mathieu Adjemout
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) U1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
| | - Bruno Pouvelle
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) U1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
| | - Fatou Thiam
- Groupe de Recherche Biotechnologie Appliquée et Bioprocédés Environnementaux (GRBA-BE), Ecole Supérieure Polytechnique, Université Cheikh Anta Diop de Dakar, Dakar BP5005, Senegal
| | - Alassane Thiam
- Pole D’Immunophysiopathologie & Maladies Infectieuses (IMI), Institut Pasteur de Dakar, Dakar BP 220, Senegal
| | - Magali Torres
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) U1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
| | - Samia Nisar
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) U1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
| | - Babacar Mbengue
- Service D’Immunologie, Université Cheikh Anta Diop de Dakar, Dakar BP5005, Senegal
| | - Alioune Dieye
- Service D’Immunologie, Université Cheikh Anta Diop de Dakar, Dakar BP5005, Senegal
| | - Pascal Rihet
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) U1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
| | - Sandrine Marquet
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) U1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
- Aix Marseille University, CNRS, Marseille 13009, France
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Cretin J, Adjemout M, Dieppois C, Gallardo F, Torres M, Merard Z, Sawadogo SA, Picard C, Rihet P, Paul P. A Non-Coding Fc Gamma Receptor Cis-Regulatory Variant within the 1q23 Gene Cluster Is Associated with Plasmodium falciparum Infection in Children Residing in Burkina Faso. Int J Mol Sci 2023; 24:15711. [PMID: 37958695 PMCID: PMC10650193 DOI: 10.3390/ijms242115711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/27/2023] [Accepted: 08/31/2023] [Indexed: 11/15/2023] Open
Abstract
Antibodies play a crucial role in activating protective immunity against malaria by interacting with Fc-gamma receptors (FcγRs). Genetic variations in genes encoding FcγRs can affect immune cell responses to the parasite. In this study, our aim was to investigate whether non-coding variants that regulate FcγR expression could influence the prevalence of Plasmodium falciparum infection. Through bioinformatics approaches, we selected expression quantitative trait loci (eQTL) for FCGR2A, FCGR2B, FCGR2C, FCGR3A, and FCGR3B genes encoding FcγRs (FCGR), in whole blood. We prioritized two regulatory variants, rs2099684 and rs1771575, located in open genomic regions. These variants were identified using RegVar, ImmuNexUT, and transcription factor annotations specific to immune cells. In addition to these, we genotyped the coding variants FCGR2A/rs1801274 and FCGR2B/rs1050501 in 234 individuals from a malaria-endemic area in Burkina Faso. We conducted age and family-based analyses to evaluate associations with the prevalence of malarial infection in both children and adults. The analysis revealed that the regulatory rs1771575-CC genotype was predicted to influence FCGR2B/FCGR2C/FCGR3A transcripts in immune cells and was the sole variant associated with a higher prevalence of malarial infection in children. In conclusion, this study identifies the rs1771575 cis-regulatory variant affecting several FcγRs in myeloid and neutrophil cells and associates it with the inter-individual capacity of children living in Burkina Faso to control malarial infection.
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Affiliation(s)
- Jules Cretin
- INSERM 1090, TAGC Theories and Approaches of Genomic Complexity, Campus de Luminy, Aix Marseille University, 13288 Marseille, France (M.A.); (C.D.); (F.G.); (M.T.)
- Institut MarMaRa, 13288 Marseille, France
| | - Mathieu Adjemout
- INSERM 1090, TAGC Theories and Approaches of Genomic Complexity, Campus de Luminy, Aix Marseille University, 13288 Marseille, France (M.A.); (C.D.); (F.G.); (M.T.)
- Institut MarMaRa, 13288 Marseille, France
| | - Christelle Dieppois
- INSERM 1090, TAGC Theories and Approaches of Genomic Complexity, Campus de Luminy, Aix Marseille University, 13288 Marseille, France (M.A.); (C.D.); (F.G.); (M.T.)
| | - Frederic Gallardo
- INSERM 1090, TAGC Theories and Approaches of Genomic Complexity, Campus de Luminy, Aix Marseille University, 13288 Marseille, France (M.A.); (C.D.); (F.G.); (M.T.)
| | - Magali Torres
- INSERM 1090, TAGC Theories and Approaches of Genomic Complexity, Campus de Luminy, Aix Marseille University, 13288 Marseille, France (M.A.); (C.D.); (F.G.); (M.T.)
| | - Zachary Merard
- ADES UMR, Aix Marseille University, 13288 Marseille, France (C.P.)
| | - Serge Aimé Sawadogo
- Unité de Formation en Sciences de la Santé (UFR/SDS), Université Joseph KI-ZERBO, Ouagadougou 03 BP 7021, Burkina Faso;
- Centre PrïmO-Nelson Mandela, 84 rue Sao Tomé et Principe, Ouagadougou 09 BP 706, Burkina Faso
| | - Christophe Picard
- ADES UMR, Aix Marseille University, 13288 Marseille, France (C.P.)
- Immunogenetics Laboratory, Etablissement Français du Sang PACA-Corse, 13001 Marseille, France
| | - Pascal Rihet
- INSERM 1090, TAGC Theories and Approaches of Genomic Complexity, Campus de Luminy, Aix Marseille University, 13288 Marseille, France (M.A.); (C.D.); (F.G.); (M.T.)
| | - Pascale Paul
- INSERM 1090, TAGC Theories and Approaches of Genomic Complexity, Campus de Luminy, Aix Marseille University, 13288 Marseille, France (M.A.); (C.D.); (F.G.); (M.T.)
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Madaci L, Gard C, Nin S, Venton G, Rihet P, Puthier D, Loriod B, Costello R. The Contribution of Multiplexing Single Cell RNA Sequencing in Acute Myeloid Leukemia. Diseases 2023; 11:96. [PMID: 37489448 PMCID: PMC10366847 DOI: 10.3390/diseases11030096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023] Open
Abstract
Decades ago, the treatment for acute myeloid leukemia relied on cytarabine and anthracycline. However, advancements in medical research have introduced targeted therapies, initially employing monoclonal antibodies such as ant-CD52 and anti-CD123, and subsequently utilizing specific inhibitors that target molecular mutations like anti-IDH1, IDH2, or FLT3. The challenge lies in determining the role of these therapeutic options, considering the inherent tumor heterogeneity associated with leukemia diagnosis and the clonal drift that this type of tumor can undergo. Targeted drugs necessitate an examination of various therapeutic targets at the individual cell level rather than assessing the entire population. It is crucial to differentiate between the prognostic value and therapeutic potential of a specific molecular target, depending on whether it is found in a terminally differentiated cell with limited proliferative potential or a stem cell with robust capabilities for both proliferation and self-renewal. However, this cell-by-cell analysis is accompanied by several challenges. Firstly, the scientific aspect poses difficulties in comparing different single cell analysis experiments despite efforts to standardize the results through various techniques. Secondly, there are practical obstacles as each individual cell experiment incurs significant financial costs and consumes a substantial amount of time. A viable solution lies in the ability to process multiple samples simultaneously, which is a distinctive feature of the cell hashing technique. In this study, we demonstrate the applicability of the cell hashing technique for analyzing acute myeloid leukemia cells. By comparing it to standard single cell analysis, we establish a strong correlation in various parameters such as quality control, gene expression, and the analysis of leukemic blast markers in patients. Consequently, this technique holds the potential to become an integral part of the biological assessment of acute myeloid leukemia, contributing to the personalized and optimized management of the disease, particularly in the context of employing targeted therapies.
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Affiliation(s)
- Lamia Madaci
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
| | - Charlyne Gard
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
| | - Sébastien Nin
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
| | - Geoffroy Venton
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
- Hematology and Cellular Therapy Department, Conception Hospital, 13005 Marseille, France
| | - Pascal Rihet
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
| | - Denis Puthier
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
| | - Béatrice Loriod
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
| | - Régis Costello
- TAGC, INSERM, UMR1090, Aix Marseille University, Parc Scientifique de Luminy, 13009 Marseille, France
- Hematology and Cellular Therapy Department, Conception Hospital, 13005 Marseille, France
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Rosier F, Nuñez NF, Torres M, Loriod B, Rihet P, Pradel LC. Transcriptional Response in a Sepsis Mouse Model Reflects Transcriptional Response in Sepsis Patients. Int J Mol Sci 2022; 23:ijms23020821. [PMID: 35055007 PMCID: PMC8776114 DOI: 10.3390/ijms23020821] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 02/06/2023] Open
Abstract
Mortality due to sepsis remains unacceptably high, especially for septic shock patients. Murine models have been used to better understand pathophysiology mechanisms. However, the mouse model is still under debate. Herein we investigated the transcriptional response of mice injected with lipopolysaccharide (LPS) and compared it to either human cells stimulated in vitro with LPS or to the blood cells of septic patients. We identified a molecular signature composed of 2331 genes with an FDR median of 0%. This molecular signature is highly enriched in regulated genes in peritoneal macrophages stimulated with LPS. There is significant enrichment in several inflammatory signaling pathways, and in disease terms, such as pneumonia, sepsis, systemic inflammatory response syndrome, severe sepsis, an inflammatory disorder, immune suppression, and septic shock. A significant overlap between the genes upregulated in mouse and human cells stimulated with LPS has been demonstrated. Finally, genes upregulated in mouse cells stimulated with LPS are enriched in genes upregulated in human cells stimulated in vitro and in septic patients, who are at high risk of death. Our results support the hypothesis of common molecular and cellular mechanisms between mouse and human sepsis.
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Affiliation(s)
| | | | | | | | - Pascal Rihet
- Correspondence: (P.R.); (L.C.P.); Tel.: +33-491828723 (P.R.); +33-491828745 (L.C.P.)
| | - Lydie C. Pradel
- Correspondence: (P.R.); (L.C.P.); Tel.: +33-491828723 (P.R.); +33-491828745 (L.C.P.)
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Rosier F, Brisebarre A, Dupuis C, Baaklini S, Puthier D, Brun C, Pradel LC, Rihet P, Payen D. Genetic Predisposition to the Mortality in Septic Shock Patients: From GWAS to the Identification of a Regulatory Variant Modulating the Activity of a CISH Enhancer. Int J Mol Sci 2021; 22:ijms22115852. [PMID: 34072601 PMCID: PMC8198806 DOI: 10.3390/ijms22115852] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
The high mortality rate in septic shock patients is likely due to environmental and genetic factors, which influence the host response to infection. Two genome-wide association studies (GWAS) on 832 septic shock patients were performed. We used integrative bioinformatic approaches to annotate and prioritize the sepsis-associated single nucleotide polymorphisms (SNPs). An association of 139 SNPs with death based on a false discovery rate of 5% was detected. The most significant SNPs were within the CISH gene involved in cytokine regulation. Among the 139 SNPs associated with death and the 1311 SNPs in strong linkage disequilibrium with them, we investigated 1439 SNPs within non-coding regions to identify regulatory variants. The highest integrative weighted score (IW-score) was obtained for rs143356980, indicating that this SNP is a robust regulatory candidate. The rs143356980 region is located in a non-coding region close to the CISH gene. A CRISPR-Cas9-mediated deletion of this region and specific luciferase assays in K562 cells showed that rs143356980 modulates the enhancer activity in K562 cells. These analyses allowed us to identify several genes associated with death in patients with septic shock. They suggest that genetic variations in key genes, such as CISH, perturb relevant pathways, increasing the risk of death in sepsis patients.
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Affiliation(s)
- Florian Rosier
- Aix Marseille Univ, INSERM, TAGC, UMR_S_1090, MarMaRa Institute, 13288 Marseille, France; (F.R.); (A.B.); (S.B.); (D.P.); (C.B.)
| | - Audrey Brisebarre
- Aix Marseille Univ, INSERM, TAGC, UMR_S_1090, MarMaRa Institute, 13288 Marseille, France; (F.R.); (A.B.); (S.B.); (D.P.); (C.B.)
| | - Claire Dupuis
- Medical Intensive Care Unit, Clermont-Ferrand University Hospital, 58 rue Montalembert, 63003 Clermont-Ferrand, France;
| | - Sabrina Baaklini
- Aix Marseille Univ, INSERM, TAGC, UMR_S_1090, MarMaRa Institute, 13288 Marseille, France; (F.R.); (A.B.); (S.B.); (D.P.); (C.B.)
| | - Denis Puthier
- Aix Marseille Univ, INSERM, TAGC, UMR_S_1090, MarMaRa Institute, 13288 Marseille, France; (F.R.); (A.B.); (S.B.); (D.P.); (C.B.)
| | - Christine Brun
- Aix Marseille Univ, INSERM, TAGC, UMR_S_1090, MarMaRa Institute, 13288 Marseille, France; (F.R.); (A.B.); (S.B.); (D.P.); (C.B.)
- CNRS, 13288 Marseille, France
| | - Lydie C. Pradel
- Aix Marseille Univ, INSERM, TAGC, UMR_S_1090, MarMaRa Institute, 13288 Marseille, France; (F.R.); (A.B.); (S.B.); (D.P.); (C.B.)
- Correspondence: (L.C.P.); (P.R.); (D.P.); Tel.: +33-491828745 (L.C.P.); +33-491828723 (P.R.); +33-687506599 (D.P.)
| | - Pascal Rihet
- Aix Marseille Univ, INSERM, TAGC, UMR_S_1090, MarMaRa Institute, 13288 Marseille, France; (F.R.); (A.B.); (S.B.); (D.P.); (C.B.)
- Correspondence: (L.C.P.); (P.R.); (D.P.); Tel.: +33-491828745 (L.C.P.); +33-491828723 (P.R.); +33-687506599 (D.P.)
| | - Didier Payen
- UMR INSERM 1160: Alloimmunité, Autoimmunité, Transplantation, University of Paris 7 Denis Diderot, 2 rue Ambroise-Paré, CEDEX 10, 75475 Paris, France
- Correspondence: (L.C.P.); (P.R.); (D.P.); Tel.: +33-491828745 (L.C.P.); +33-491828723 (P.R.); +33-687506599 (D.P.)
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9
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Thiam A, Sanka M, Ndiaye Diallo R, Torres M, Mbengue B, Nunez NF, Thiam F, Diop G, Victorero G, Nguyen C, Dieye A, Rihet P. Gene expression profiling in blood from cerebral malaria patients and mild malaria patients living in Senegal. BMC Med Genomics 2019; 12:148. [PMID: 31666081 PMCID: PMC6821028 DOI: 10.1186/s12920-019-0599-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 10/09/2019] [Indexed: 01/06/2023] Open
Abstract
Background Plasmodium falciparum malaria remains a major health problem in Africa. The mechanisms of pathogenesis are not fully understood. Transcriptomic studies may provide new insights into molecular pathways involved in the severe form of the disease. Methods Blood transcriptional levels were assessed in patients with cerebral malaria, non-cerebral malaria, or mild malaria by using microarray technology to look for gene expression profiles associated with clinical status. Multi-way ANOVA was used to extract differentially expressed genes. Network and pathways analyses were used to detect enrichment for biological pathways. Results We identified a set of 443 genes that were differentially expressed in the three patient groups after applying a false discovery rate of 10%. Since the cerebral patients displayed a particular transcriptional pattern, we focused our analysis on the differences between cerebral malaria patients and mild malaria patients. We further found 842 differentially expressed genes after applying a false discovery rate of 10%. Unsupervised hierarchical clustering of cerebral malaria-informative genes led to clustering of the cerebral malaria patients. The support vector machine method allowed us to correctly classify five out of six cerebral malaria patients and six of six mild malaria patients. Furthermore, the products of the differentially expressed genes were mapped onto a human protein-protein network. This led to the identification of the proteins with the highest number of interactions, including GSK3B, RELA, and APP. The enrichment analysis of the gene functional annotation indicates that genes involved in immune signalling pathways play a role in the occurrence of cerebral malaria. These include BCR-, TCR-, TLR-, cytokine-, FcεRI-, and FCGR- signalling pathways and natural killer cell cytotoxicity pathways, which are involved in the activation of immune cells. In addition, our results revealed an enrichment of genes involved in Alzheimer’s disease. Conclusions In the present study, we examine a set of genes whose expression differed in cerebral malaria patients and mild malaria patients. Moreover, our results provide new insights into the potential effect of the dysregulation of gene expression in immune pathways. Host genetic variation may partly explain such alteration of gene expression. Further studies are required to investigate this in African populations.
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Affiliation(s)
- Alassane Thiam
- Unité d'Immunogénétique, Institut Pasteur de Dakar, Dakar, Sénégal
| | - Michel Sanka
- Aix Marseille Univ, INSERM, TAGC UMR U1090, 163 Av de Luminy, 13288, Marseille, cedex 9, France
| | - Rokhaya Ndiaye Diallo
- Service de Génétique Humaine, Faculté de Médecine, de Pharmacie et d'Odontostomatologie, UCAD, Dakar, Sénégal
| | - Magali Torres
- Aix Marseille Univ, INSERM, TAGC UMR U1090, 163 Av de Luminy, 13288, Marseille, cedex 9, France
| | - Babacar Mbengue
- Service Immunologie, Faculte de Medecine, Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Nicolas Fernandez Nunez
- Aix Marseille Univ, INSERM, TAGC UMR U1090, 163 Av de Luminy, 13288, Marseille, cedex 9, France
| | - Fatou Thiam
- Département de Génie chimique et biologie, Ecole Supérieure Polytechnique, Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Gora Diop
- Unité d'Immunogénétique, Institut Pasteur de Dakar, Dakar, Sénégal.,Département de Biologie animale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Geneviève Victorero
- Aix Marseille Univ, INSERM, TAGC UMR U1090, 163 Av de Luminy, 13288, Marseille, cedex 9, France
| | - Catherine Nguyen
- Aix Marseille Univ, INSERM, TAGC UMR U1090, 163 Av de Luminy, 13288, Marseille, cedex 9, France
| | - Alioune Dieye
- Unité d'Immunogénétique, Institut Pasteur de Dakar, Dakar, Sénégal.,Service Immunologie, Faculte de Medecine, Université Cheikh Anta Diop de Dakar, Dakar, Sénégal
| | - Pascal Rihet
- Aix Marseille Univ, INSERM, TAGC UMR U1090, 163 Av de Luminy, 13288, Marseille, cedex 9, France.
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10
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González A, Artufel M, Rihet P. TAGOOS: genome-wide supervised learning of non-coding loci associated to complex phenotypes. Nucleic Acids Res 2019; 47:e79. [PMID: 31045203 PMCID: PMC6698643 DOI: 10.1093/nar/gkz320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/07/2019] [Accepted: 04/18/2019] [Indexed: 01/04/2023] Open
Abstract
Genome-wide association studies (GWAS) associate single nucleotide polymorphisms (SNPs) to complex phenotypes. Most human SNPs fall in non-coding regions and are likely regulatory SNPs, but linkage disequilibrium (LD) blocks make it difficult to distinguish functional SNPs. Therefore, putative functional SNPs are usually annotated with molecular markers of gene regulatory regions and prioritized with dedicated prediction tools. We integrated associated SNPs, LD blocks and regulatory features into a supervised model called TAGOOS (TAG SNP bOOSting) and computed scores genome-wide. The TAGOOS scores enriched and prioritized unseen associated SNPs with an odds ratio of 4.3 and 3.5 and an area under the curve (AUC) of 0.65 and 0.6 for intronic and intergenic regions, respectively. The TAGOOS score was correlated with the maximal significance of associated SNPs and expression quantitative trait loci (eQTLs) and with the number of biological samples annotated for key regulatory features. Analysis of loci and regions associated to cleft lip and human adult height phenotypes recovered known functional loci and predicted new functional loci enriched in transcriptions factors related to the phenotypes. In conclusion, we trained a supervised model based on associated SNPs to prioritize putative functional regions. The TAGOOS scores, annotations and UCSC genome tracks are available here: https://tagoos.readthedocs.io.
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Affiliation(s)
- Aitor González
- Aix Marseille Univ, INSERM, TAGC, Turing Center for Living Systems, 13288 Marseille, France
| | - Marie Artufel
- Aix Marseille Univ, INSERM, TAGC, Turing Center for Living Systems, 13288 Marseille, France
| | - Pascal Rihet
- Aix Marseille Univ, INSERM, TAGC, Turing Center for Living Systems, 13288 Marseille, France
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11
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Thiam A, Baaklini S, Mbengue B, Nisar S, Diarra M, Marquet S, Fall MM, Sanka M, Thiam F, Diallo RN, Torres M, Dieye A, Rihet P. NCR3 polymorphism, haematological parameters, and severe malaria in Senegalese patients. PeerJ 2018; 6:e6048. [PMID: 30533319 PMCID: PMC6282937 DOI: 10.7717/peerj.6048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/31/2018] [Indexed: 12/12/2022] Open
Abstract
Background Host factors, including host genetic variation, have been shown to influence the outcome of Plasmodium falciparum infection. Genome-wide linkage studies have mapped mild malaria resistance genes on chromosome 6p21, whereas NCR3-412 polymorphism (rs2736191) lying within this region was found to be associated with mild malaria. Methods Blood samples were taken from 188 Plasmodium falciparum malaria patients (76 mild malaria patients, 85 cerebral malaria patients, and 27 severe non-cerebral malaria patients). NCR3-412 (rs2736191) was analysed by sequencing, and haematological parameters were measured. Finally, their association with clinical phenotypes was assessed. Results We evidenced an association of thrombocytopenia with both cerebral malaria and severe non-cerebral malaria, and of an association of high leukocyte count with cerebral malaria. Additionally, we found no association of NCR3-412 with either cerebral malaria, severe non-cerebral malaria, or severe malaria after grouping cerebral malaria and severe non-cerebral malaria patients. Conclusions Our results suggest that NCR3 genetic variation has no effect, or only a small effect on the occurrence of severe malaria, although it has been strongly associated with mild malaria. We discuss the biological meaning of these results. Besides, we confirmed the association of thrombocytopenia and high leukocyte count with severe malaria phenotypes.
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Affiliation(s)
- Alassane Thiam
- Unité d'Immunogénétique, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Babacar Mbengue
- Service d'Immunologie, University Cheikh Anta Diop of Dakar, Dakar, Senegal
| | - Samia Nisar
- Aix Marseille Univ, INSERM, TAGC, Marseille, France
| | - Maryam Diarra
- G4 Biostatistique, Institut Pasteur de Dakar, Dakar, Sénégal
| | | | | | - Michel Sanka
- Aix Marseille Univ, INSERM, TAGC, Marseille, France
| | - Fatou Thiam
- Unité d'Immunogénétique, Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | - Alioune Dieye
- Unité d'Immunogénétique, Institut Pasteur de Dakar, Dakar, Senegal.,Service d'Immunologie, University Cheikh Anta Diop of Dakar, Dakar, Senegal
| | - Pascal Rihet
- Aix Marseille Univ, INSERM, TAGC, Marseille, France
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12
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Nguyen NT, Vivès RR, Torres M, Delauzun V, Saesen E, Roig-Zamboni V, Lortat-Jacob H, Rihet P, Bourne Y. Genetic and enzymatic characterization of 3-O-sulfotransferase SNPs associated with Plasmodium falciparum parasitaemia. Glycobiology 2018; 28:534-541. [PMID: 29718295 DOI: 10.1093/glycob/cwy038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/27/2018] [Indexed: 01/09/2023] Open
Abstract
The HS3ST3A1/B1 genes encode two homologous 3-O-sulfotransferases involved in the late modification step during heparan sulfate (HS) biosynthesis. In addition to the single nucleotide polymorphisms (SNPs) rs28470223 (C > T) in the promoter region of both HS3ST3A1 and rs62636623 (Gly/Arg) in the stem region of HS3ST3B1, three missense mutations (rs62056073, rs61729712 and rs9906590) located within the catalytic sulfotransferase domain of 3-OST-B1 are linked and associated to Plasmodium falciparum parasitaemia. To ascertain the functional effects of these SNP associations, we investigated the regulatory effect of rs28470223 and characterized the enzymatic activity of the missense SNP rs61729712 (Ser279Asn) localized at proximity of the substrate binding cleft. The SNP rs28470223 results in decreased promoter activity of HS3ST3A1 in K562 cells, suggesting a reduced in vivo transcription activity of the target gene. A comparative kinetic analysis of wt HS3ST3B1 and the Ser269Asn variant (rs61729712) using a HS-derived oligosaccharide substrate reveals a slightly higher catalytic activity for the SNP variant. These genetic and enzymatic studies suggest that genetic variations in enzymes responsible of HS 3-O-sulfation can modulate their promoter and enzymatic activities and may influence P. falciparum parasitaemia.
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Affiliation(s)
- Ngoc Thy Nguyen
- Aix Marseille University, INSERM, TAGC, Marseille, France.,CNRS, Aix Marseille University, AFMB, Marseille, France
| | - Romain R Vivès
- University of Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Magali Torres
- Aix Marseille University, INSERM, TAGC, Marseille, France
| | | | - Els Saesen
- University of Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | | | - Pascal Rihet
- Aix Marseille University, INSERM, TAGC, Marseille, France
| | - Yves Bourne
- CNRS, Aix Marseille University, AFMB, Marseille, France
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13
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Choquet C, Nguyen THM, Sicard P, Buttigieg E, Tran TT, Kober F, Varlet I, Sturny R, Costa MW, Harvey RP, Nguyen C, Rihet P, Richard S, Bernard M, Kelly RG, Lalevée N, Miquerol L. Correction: Deletion of Nkx2-5 in trabecular myocardium reveals the developmental origins of pathological heterogeneity associated with ventricular non-compaction cardiomyopathy. PLoS Genet 2018; 14:e1007610. [PMID: 30110325 PMCID: PMC6093597 DOI: 10.1371/journal.pgen.1007610] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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14
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Labiad Y, Venton G, Farnault L, Baier C, Colle J, Mercier C, Ivanov V, Nicolino C, Loriod B, Fernandez-Nunez N, Torres M, Mattei JC, Rihet P, Nguyen C, Costello R. A transcriptomic signature predicting septic outcome in patients undergoing autologous stem cell transplantation. Exp Hematol 2018; 65:49-56. [PMID: 29885947 DOI: 10.1016/j.exphem.2018.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/25/2018] [Accepted: 06/03/2018] [Indexed: 11/26/2022]
Abstract
Autologous hematopoietic stem cell transplantation is the standard treatment for multiple myeloma and relapsed or refractory lymphomas. After autologous hematopoietic stem cell transplantation, hematologic reconstitution and infectious complications are the two most critical issues. Although many patients develop infectious complications after therapeutic intensification, it remains impossible to predict infection for each individual. The goal of this work was to determine and identify a predictive transcriptomic signature of systemic inflammatory response syndrome and/or sepsis in patients receiving autologous hematopoietic stem cell transplantation. High-throughput transcriptomic and bioinformatics analysis were performed to analyze gene expression modulation in peripheral blood mononuclear cells in 21 patients undergoing autologous hematopoietic stem cell transplantation for hematological malignancies (lymphoma or multiple myeloma). Transcriptomic analysis of peripheral blood mononuclear cells samples collected just after conditioning regimen identified an 11-gene signature (CHAT, CNN3, ANKRD42, LOC100505725, EDAR, GPAT2, ENST00000390425, MTRM8, C6orf192, LOC10289230, and XLOC-005643) that was able to early predict (at least 2-7 days before its occurrence) the development of systemic inflammatory response syndrome or sepsis. The possibility of systemic inflammatory response syndrome or sepsis occurrence early prediction (2-7 days before occurrence) opens up new therapeutic strategies based on preemptive antibiotic and/or antifungal prophylaxis adapted to the specific risk profile of each patient.
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Affiliation(s)
- Yasmine Labiad
- Aix Marseille University, INSERM, TAGC, Marseille, France
| | - Geoffroy Venton
- Assistance Publique des Hôpitaux de Marseille, Service d'Hématologie et de Thérapie Cellulaire de La Conception, Marseille, France
| | - Laure Farnault
- Assistance Publique des Hôpitaux de Marseille, Service d'Hématologie et de Thérapie Cellulaire de La Conception, Marseille, France
| | - Céline Baier
- Aix Marseille University, INSERM, TAGC, Marseille, France
| | - Julien Colle
- Aix Marseille University, INSERM, TAGC, Marseille, France; Assistance Publique des Hôpitaux de Marseille, Service d'Hématologie et de Thérapie Cellulaire de La Conception, Marseille, France
| | - Cédric Mercier
- Assistance Publique des Hôpitaux de Marseille, Service d'Hématologie et de Thérapie Cellulaire de La Conception, Marseille, France
| | - Vadim Ivanov
- Assistance Publique des Hôpitaux de Marseille, Service d'Hématologie et de Thérapie Cellulaire de La Conception, Marseille, France
| | - Corinne Nicolino
- Assistance Publique des Hôpitaux de Marseille, Service d'Hématologie et de Thérapie Cellulaire de La Conception, Marseille, France
| | | | | | - Magali Torres
- Aix Marseille University, INSERM, TAGC, Marseille, France
| | | | - Pascal Rihet
- Assistance Publique des Hôpitaux de Marseille, Service d'Hématologie et de Thérapie Cellulaire de La Conception, Marseille, France
| | | | - Régis Costello
- Aix Marseille University, INSERM, TAGC, Marseille, France; Assistance Publique des Hôpitaux de Marseille, Service d'Hématologie et de Thérapie Cellulaire de La Conception, Marseille, France.
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15
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Nguyen TN, Baaklini S, Koukouikila-Koussounda F, Ndounga M, Torres M, Pradel L, Ntoumi F, Rihet P. Association of a functional TNF variant with Plasmodium falciparum parasitaemia in a congolese population. Genes Immun 2017; 18:152-157. [DOI: 10.1038/gene.2017.13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/08/2017] [Accepted: 05/10/2017] [Indexed: 11/09/2022]
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16
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Ragheb R, Venton G, Chelbi R, Bonnet N, Le Treut T, Ivanov V, Mercier C, Poulin P, Beaufils N, Gabert J, Suchon P, Rihet P, Loriod B, Kahn-Perlès B, Costello RT. Vorinostat and Mithramycin A in combination therapy as an interesting strategy for the treatment of Sézary T lymphoma: a transcriptomic approach. Arch Dermatol Res 2017; 309:611-623. [PMID: 28695331 DOI: 10.1007/s00403-017-1761-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/07/2017] [Accepted: 07/03/2017] [Indexed: 12/22/2022]
Abstract
SAHA (vorinostat) is a histone deacetylase inhibitor approved by the USA Food and Drug Administration (FDA) for treating advanced refractory cutaneous T cell lymphomas. As SAHA alters the expression of many genes under control of the Sp1 transcription factor, we examined the effect of its association with the FDA-approved anticancer antibiotic Mithramycin A (MTR, plicamycin), a competitive inhibitor of Sp1 binding to DNA. Sézary syndrome (SS) cells, expanded ex vivo from peripheral blood mononuclear cells of 4 patients, were tested for their sensitivity to the drugs regarding cytotoxicity and differential responsive gene expression. Multivariate statistical methods were used to identify genes whose expression is altered by SAHA, MTR, and the synergist effect of the two drugs. MTR, like SAHA, induced the apoptosis of SS cells, while the two drugs in combination showed clear synergy or potentiation. Expression data stressed a likely important role of additive or synergistic epigenetic modifications in the combined effect of the two drugs, while direct inhibition of Sp1-dependent transcription seemed to have only limited impact. Ontological analysis of modified gene expression suggested that the two drugs, either independently or synergistically, counteracted many intertwined pro-survival pathways deregulated in SS cells, resistance of these tumors to intrinsic and extrinsic apoptosis, abnormal adhesion migration, and invasive properties, as well as immunosuppressive behavior. Our findings provide preliminary clues on the individual and combined effects of SAHA and MTR in SS cells and highlight a potential therapeutic interest of this novel pair of drugs for treatment of SS patients.
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Affiliation(s)
- R Ragheb
- Aix Marseille Université, INSERM UMR_S 1090, Technological Advances for Genomics and Clinics, 13288, Marseille-Luminy, France
| | - G Venton
- Aix Marseille Université, INSERM UMR_S 1090, Technological Advances for Genomics and Clinics, 13288, Marseille-Luminy, France.,Assistance Publique des Hôpitaux de Marseille, Hôpital de la Conception, Service d'Hématologie et de Thérapie Cellulaire, 13005, Marseille, France
| | - R Chelbi
- Aix Marseille Université, INSERM UMR_S 1090, Technological Advances for Genomics and Clinics, 13288, Marseille-Luminy, France
| | - N Bonnet
- Assistance Publique Hôpitaux de Marseille, Hôpital Nord, Service de Dermatologie, 13915, Marseille, France
| | - T Le Treut
- Assistance Publique Hôpitaux de Marseille, Hôpital Nord, Laboratoire d'Hématologie, 13915, Marseille, France
| | - V Ivanov
- Assistance Publique des Hôpitaux de Marseille, Hôpital de la Conception, Service d'Hématologie et de Thérapie Cellulaire, 13005, Marseille, France
| | - C Mercier
- Assistance Publique des Hôpitaux de Marseille, Hôpital de la Conception, Service d'Hématologie et de Thérapie Cellulaire, 13005, Marseille, France
| | - P Poulin
- Assistance Publique Hôpitaux de Marseille, Hôpital La Conception, Service d'Hémaphérèse, 13005, Marseille, France
| | - N Beaufils
- Assistance Publique des Hôpitaux de Marseille, Hôpital Nord, Laboratoire de Biochimie Biologie Moléculaire, 13288, Marseille, France
| | - J Gabert
- Assistance Publique des Hôpitaux de Marseille, Hôpital Nord, Laboratoire de Biochimie Biologie Moléculaire, 13288, Marseille, France
| | - P Suchon
- Assistance Publique des Hôpitaux de Marseille, Hôpital de la Timone, Service d'Hématologie, 13005, Marseille, France
| | - P Rihet
- Aix Marseille Université, INSERM UMR_S 1090, Technological Advances for Genomics and Clinics, 13288, Marseille-Luminy, France
| | - B Loriod
- Aix Marseille Université, INSERM UMR_S 1090, Technological Advances for Genomics and Clinics, 13288, Marseille-Luminy, France
| | - B Kahn-Perlès
- Aix Marseille Université, INSERM UMR_S 1090, Technological Advances for Genomics and Clinics, 13288, Marseille-Luminy, France
| | - Régis T Costello
- Aix Marseille Université, INSERM UMR_S 1090, Technological Advances for Genomics and Clinics, 13288, Marseille-Luminy, France. .,Assistance Publique des Hôpitaux de Marseille, Hôpital de la Conception, Service d'Hématologie et de Thérapie Cellulaire, 13005, Marseille, France.
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17
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Nguyen M, Choquet C, Sicard P, Kober F, Varlet I, Rihet P, Richard S, Nguyen C, Bernard M, Kelly R, Lalevée N, Miquerol L. Temporal deletions of Nkx2-5 induce hypertrabeculation and progressive conduction defects and heart failure. Archives of Cardiovascular Diseases Supplements 2017. [DOI: 10.1016/s1878-6480(17)30515-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Ingles M, Crowfoot G, Smelaya TV, Kuzovlev AN, Salnikova LE, Bhikoo R, Khwannimit B, Bhurayanontachai R, Vattanavanit V, Tourteau E, Filali A, van Grunderbeeck N, Nigeon O, Bazus H, Masse J, Mallat J, Thevenin D, Prokhorenko I, Kabanov D, Zubova S, Grachev S, Salcedo M, Witte S, Cuvier V, Derive M, Gibot S, Garaud JJ, Kumar V, Chhibber S, Santos JR, Sevillejal JEAD, Nevado JB, Linge HM, Ochani K, Lin K, Lee JY, Wang P, Tembhre M, Liu SF, Singhal PC, Miller EJ, HO J, Liu X, Kwong T, Zhang L, Chan H, Wong SH, Choi G, Gin T, Chan MTV, Wu WKK, Vliegen G, Kehoe K, Verkerk R, Fransen E, Peters E, Lambeir AM, Pickkers P, Jorens PG, De Meester I, Ribeiro AB, Souza APT, Giusti H, Franci CR, Saia RS, Anderko RR, Jackson VM, Palmer OMP, Angus DC, Kellum JA, Carcillo JA, Verboom DM, Koster-Brouwer ME, van de Groep K, Frencken JF, Scicluna B, Gisbertz SS, Henegouwen MIVB, Ruurda JP, van Hillegersberg R, van der Poll T, Bonten MJM, Cremer OL, Verboom DM, Frencken JF, van der Poll T, Bonten MJM, Cremer OL, Klouwenberg PMCK, Beloborodova N, Osipov A, Pautova A, Bedova A, Mas-Oliva J, García-González V, Sukhina M, Zhukhovitskiy V, Sukhina MA, Obraztsov I, Zhukhovitskiy VG, Peronace C, Matera G, Galati L, Giancotti A, Barreca GS, Quirino A, Liberto MC, Focà A, Labiad Y, Venton G, Baier C, Colle J, Farnault L, Brunet C, Loriod B, Fernandez-Nunez N, Suchon P, Mattei JC, Rihet P, Nguyen C, Costello R, Tesfai A, Ahmetaj-Shala B, Gashaw H, Quinlan G, MacCallum N, Mumby S, Gray DN, Leiper J, Kirkby N, Mitchell JA, Costa LHA, Catalão CHR, Santos-Júnior NN, Souza AO, Alberici LC, Rocha MJA. Sepsis 2016 Paris. Crit Care 2016. [PMCID: PMC5260789 DOI: 10.1186/s13054-016-1518-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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19
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Sanchez C, Baier C, Colle JG, Chelbi R, Rihet P, Le Treut T, Imbert J, Sébahoun G, Venton G, Costello RT. Natural killer cells in patients with polycythemia vera. Hum Immunol 2015; 76:644-50. [PMID: 26407910 DOI: 10.1016/j.humimm.2015.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 07/24/2015] [Accepted: 09/21/2015] [Indexed: 01/08/2023]
Abstract
Natural killer cells (NK) are pivotal cells of innate immunity. They are potent antileukemic cytotoxic effectors. A defect in their cytotoxicity has been described in some hematopoietic malignancies such as acute myeloid leukemia, multiple myeloma and myelodysplastic syndromes. This defect is at least partially linked to a decreased or absent expression of some activating NK cells molecules, more particularly the so-called natural cytotoxicity receptors. In the present study, we more particularly focused our attention on NK cells of polycythemia vera, a myeloproliferative disease characterized by the presence of mutated JAK2 tyrosine kinase. The polymerase chain reaction analysis of NK cells from patients showed that they expressed the mutated form of JAK2. In polycythemia vera the proportion of NK was increased compared to healthy donors. The proliferative and cytotoxic abilities of NK cells from patients were similar to healthy donors. Expression of activating or inhibitory receptors was comparable in patients and donors, with nonetheless an imbalance for the inhibitory form of the CD158a,h couple of receptors in patients. Finally, the transcriptomic profile analysis clearly identified a discriminant signature between NK cells from patients and donors that could putatively be the consequence of abnormal continuous activation of mutated JAK2.
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Affiliation(s)
- Carole Sanchez
- Aix-Marseille Université, UMR 1090 TAGC, Marseille, France; AP-HM, Hôpital de La Conception, Service d'Hématologie et Thérapie Cellulaire, Marseille, France; AP-HM, Laboratoire d'Hématologie, Hôpital Nord, Marseille, France; Laboratoire de Biologie Médicale, Centre Hospitalier, Salon de Provence, France
| | - Céline Baier
- Aix-Marseille Université, UMR 1090 TAGC, Marseille, France
| | - Julien G Colle
- Aix-Marseille Université, UMR 1090 TAGC, Marseille, France; AP-HM, Hôpital de La Conception, Service d'Hématologie et Thérapie Cellulaire, Marseille, France
| | - Rabie Chelbi
- Aix-Marseille Université, UMR 1090 TAGC, Marseille, France
| | - Pascal Rihet
- Aix-Marseille Université, UMR 1090 TAGC, Marseille, France
| | - Thérèse Le Treut
- AP-HM, Laboratoire d'Hématologie, Hôpital Nord, Marseille, France
| | - Jean Imbert
- Aix-Marseille Université, UMR 1090 TAGC, Marseille, France
| | - Gérard Sébahoun
- AP-HM, Hôpital de La Conception, Service d'Hématologie et Thérapie Cellulaire, Marseille, France; AP-HM, Laboratoire d'Hématologie, Hôpital Nord, Marseille, France
| | - Geoffroy Venton
- Aix-Marseille Université, UMR 1090 TAGC, Marseille, France; AP-HM, Hôpital de La Conception, Service d'Hématologie et Thérapie Cellulaire, Marseille, France
| | - Régis T Costello
- Aix-Marseille Université, UMR 1090 TAGC, Marseille, France; AP-HM, Hôpital de La Conception, Service d'Hématologie et Thérapie Cellulaire, Marseille, France; AP-HM, Laboratoire d'Hématologie, Hôpital Nord, Marseille, France.
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20
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Rommelaere S, Millet V, Rihet P, Atwell S, Helfer E, Chasson L, Beaumont C, Chimini G, Sambo MDR, Viallat A, Penha-Gonçalves C, Galland F, Naquet P. Serum pantetheinase/vanin levels regulate erythrocyte homeostasis and severity of malaria. Am J Pathol 2015; 185:3039-52. [PMID: 26343328 DOI: 10.1016/j.ajpath.2015.07.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 06/18/2015] [Accepted: 07/16/2015] [Indexed: 11/16/2022]
Abstract
Tissue pantetheinase, encoded by the VNN1 gene, regulates response to stress, and previous studies have shown that VNN genes contribute to the susceptibility to malaria. Herein, we evaluated the role of pantetheinase on erythrocyte homeostasis and on the development of malaria in patients and in a new mouse model of pantetheinase insufficiency. Patients with cerebral malaria have significantly reduced levels of serum pantetheinase activity (PA). In mouse, we show that a reduction in serum PA predisposes to severe malaria, including cerebral malaria and severe anemia. Therefore, scoring pantetheinase in serum may serve as a severity marker in malaria infection. This disease triggers an acute stress in erythrocytes, which enhances cytoadherence and hemolysis. We speculated that serum pantetheinase might contribute to erythrocyte resistance to stress under homeostatic conditions. We show that mutant mice with a reduced serum PA are anemic and prone to phenylhydrazine-induced anemia. A cytofluorometric and spectroscopic analysis documented an increased frequency of erythrocytes with an autofluorescent aging phenotype. This is associated with an enhanced oxidative stress and shear stress-induced hemolysis. Red blood cell transfer and bone marrow chimera experiments show that the aging phenotype is not cell intrinsic but conferred by the environment, leading to a shortening of red blood cell half-life. Therefore, serum pantetheinase level regulates erythrocyte life span and modulates the risk of developing complicated malaria.
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Affiliation(s)
- Samuel Rommelaere
- Immunology Center of Marseille-Luminy, Aix Marseille Université (UM2), the National Institute of Health and Medical Research INSERM U1104, the Centre National de la Recherche Scientifique CNRS UMR7280, Marseille, France
| | - Virginie Millet
- Immunology Center of Marseille-Luminy, Aix Marseille Université (UM2), the National Institute of Health and Medical Research INSERM U1104, the Centre National de la Recherche Scientifique CNRS UMR7280, Marseille, France
| | - Pascal Rihet
- Technological Advances for Genomics and Clinics (TAGC), Aix-Marseille Université, UMR_S 1090, INSERM U1090, Marseille, France
| | - Scott Atwell
- Marseilles Interdisciplinary Nanoscience Centre, Aix-Marseille Université, CNRS UMR7325, Marseille, France
| | - Emmanuèle Helfer
- Marseilles Interdisciplinary Nanoscience Centre, Aix-Marseille Université, CNRS UMR7325, Marseille, France
| | - Lionel Chasson
- Immunology Center of Marseille-Luminy, Aix Marseille Université (UM2), the National Institute of Health and Medical Research INSERM U1104, the Centre National de la Recherche Scientifique CNRS UMR7280, Marseille, France
| | - Carole Beaumont
- Biomedical Research Center Bichat-Beaujon, Université Paris Diderot, INSERM U773, Paris, France
| | - Giovanna Chimini
- Immunology Center of Marseille-Luminy, Aix Marseille Université (UM2), the National Institute of Health and Medical Research INSERM U1104, the Centre National de la Recherche Scientifique CNRS UMR7280, Marseille, France
| | | | - Annie Viallat
- Marseilles Interdisciplinary Nanoscience Centre, Aix-Marseille Université, CNRS UMR7325, Marseille, France
| | | | - Franck Galland
- Immunology Center of Marseille-Luminy, Aix Marseille Université (UM2), the National Institute of Health and Medical Research INSERM U1104, the Centre National de la Recherche Scientifique CNRS UMR7280, Marseille, France.
| | - Philippe Naquet
- Immunology Center of Marseille-Luminy, Aix Marseille Université (UM2), the National Institute of Health and Medical Research INSERM U1104, the Centre National de la Recherche Scientifique CNRS UMR7280, Marseille, France.
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21
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Metzler-Guillemain C, Victorero G, Lepoivre C, Bergon A, Yammine M, Perrin J, Sari-Minodier I, Boulanger N, Rihet P, Nguyen C. Sperm mRNAs and microRNAs as candidate markers for the impact of toxicants on human spermatogenesis: an application to tobacco smoking. Syst Biol Reprod Med 2015; 61:139-49. [PMID: 25821920 DOI: 10.3109/19396368.2015.1022835] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Spermatozoa contain a complex population of RNAs including messenger RNAs (mRNAs) and small RNAs such as microRNAs (miRNA). It has been reported that these RNAs can be used to understand the mechanisms by which toxicological exposure affects spermatogenesis. The aim of our study was to compare mRNA and miRNA profiles in spermatozoa from eight smokers and eight non-smokers, and search for potential relationships between mRNA and miRNA variation. All men were selected based on their answers to a standard toxic exposure questionnaire, and sperm parameters. Using mRNA and miRNA microarrays, we showed that mRNAs from 15 genes were differentially represented between smokers and non-smokers (p<0.01): five had higher levels and 10 lower levels in the smokers. For the microRNAs, 23 were differentially represented: 16 were higher and seven lower in the smokers (0.004≤p<0.01). Quantitative RT-PCR confirmed the lower levels in smokers compared to non-smokers for hsa-miR-296-5p, hsa-miR-3940, and hsa-miR-520d-3p. Moreover, we observed an inverse relationship between the levels of microRNAs and six potential target mRNAs (B3GAT3, HNRNPL, OASL, ODZ3, CNGB1, and PKD2). Our results indicate that alterations in the level of a small number of microRNAs in response to smoking may contribute to changes in mRNA expression in smokers. We conclude that large-scale analysis of spermatozoa RNAs can be used to help understand the mechanisms by which human spermatogenesis responds to toxic substances including those in tobacco smoke.
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22
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Bouchet A, Sakakini N, Atifi ME, Le Clec'h C, Bräuer-Krisch E, Rogalev L, Laissue JA, Rihet P, Le Duc G, Pelletier L. Identification of AREG and PLK1 pathway modulation as a potential key of the response of intracranial 9L tumor to microbeam radiation therapy. Int J Cancer 2015; 136:2705-16. [PMID: 25382544 DOI: 10.1002/ijc.29318] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 10/12/2014] [Accepted: 10/28/2014] [Indexed: 01/17/2023]
Abstract
Synchrotron microbeam radiation therapy (MRT) relies on the spatial fractionation of a synchrotron beam into parallel micron-wide beams allowing deposition of hectogray doses. MRT controls the intracranial tumor growth in rodent models while sparing normal brain tissues. Our aim was to identify the early biological processes underlying the differential effect of MRT on tumor and normal brain tissues. The expression of 28,000 transcripts was tested by microarray 6 hr after unidirectional MRT (400 Gy, 50 µm-wide microbeams, 200 µm spacing). The specific response of tumor tissues to MRT consisted in the significant transcriptomic modulation of 431 probesets (316 genes). Among them, 30 were not detected in normal brain tissues, neither before nor after MRT. Areg, Trib3 and Nppb were down-regulated, whereas all others were up-regulated. Twenty-two had similar expression profiles during the 2 weeks observed after MRT, including Ccnb1, Cdc20, Pttg1 and Plk1 related to the mitotic role of the Polo-like kinase (Plk) pathway. The up-regulation of Areg expression may indicate the emergence of survival processes in tumor cells triggered by the irradiation; while the modulation of the "mitotic role of Plk1" pathway, which relates to cytokinetic features of the tumor observed histologically after MRT, may partially explain the control of tumor growth by MRT. The identification of these tumor-specific responses permit to consider new strategies that might potentiate the antitumoral effect of MRT.
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Affiliation(s)
- Audrey Bouchet
- INSERM U836, Team Nanomedicine and brain, 6 Rue Fortuné Ferrini, F38706, La Tronche, France; Biomedical Beamline, European Synchrotron Radiation Facility, BP220, F38043, Grenoble cedex 9, France
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23
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Geiger A, Tchicaya B, Rihet P. Technical data of the transcriptomic analysis performed on tsetse fly symbionts, Sodalis glossinidius and Wigglesworthia glossinidia, harbored, respectively by non-infected, Trypanosoma brucei gambiense infected and self-cured Glossina palpalis gambiensis tsetse flies. Genom Data 2015; 4:133-6. [PMID: 26484198 PMCID: PMC4535939 DOI: 10.1016/j.gdata.2015.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 04/06/2015] [Indexed: 12/03/2022]
Abstract
Microarray is a powerful and cheap method to identify and quantify gene expression in particular in a mix of total RNA extracted from biological samples such as the tsetse fly gut, including several organisms (here, the fly tissue and the intestinal microorganisms). Besides, biostatistics and bioinformatics allow comparing the transcriptomes from samples collected from differently treated flies, and thus to identify and quantify differential expressed genes. Here, we describe in details a whole microarray transcriptome dataset produced from tsetse flies symbionts, Sodalis glossinidius and Wigglesworthia glossinidia. The tsetse fly midguts were sampled at key steps of tsetse fly infection by trypanosomes, 3-day and 10-day sampling times to target differentially expressed genes involved, respectively, in early events associated with trypanosome entry into the midgut and with the establishment of infection; 20 days to target the genes involved in events occurring later in the infection process. We describe in detail the methodology applied for analyzing the microarray data including differential expression as well as functional annotation of the identified symbiont genes. Both the microarray data and design are available at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48360;http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48361;http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55931.
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Affiliation(s)
- Anne Geiger
- UMR 177, IRD-CIRAD, CIRAD TA A-17/G, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Bernadette Tchicaya
- UMR 177, IRD-CIRAD, CIRAD TA A-17/G, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Pascal Rihet
- UMR1090 TAGC, INSERM, Marseille F-13288, France ; Aix-Marseille University, Marseille F-13288, France
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24
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Brisebarre A, Kumulungui B, Sawadogo S, Afridi S, Fumoux F, Rihet P. Genome-wide significant linkage to IgG subclass responses against Plasmodium falciparum antigens on chromosomes 8p22-p21, 9q34 and 20q13. Genes Immun 2014; 16:187-92. [PMID: 25521226 DOI: 10.1038/gene.2014.66] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 10/16/2014] [Accepted: 10/16/2014] [Indexed: 11/09/2022]
Abstract
A genome-wide scan was conducted for the levels of total immunoglobulin G (IgG) and IgG subclasses directed against Plasmodium falciparum antigens in an urban population living in Burkina Faso. Non-parametric multipoint linkage analysis provided three chromosomal regions with genome-wide significant evidence (logarithm of the odds (LOD) score >3.6), and five chromosomal regions with genome-wide suggestive evidence (LOD score >2.2). IgG3 levels were significantly linked to chromosomes 8p22-p21 and 20q13, whereas IgG4 levels were significantly linked to chromosome 9q34. In addition, we detected suggestive linkage of IgG1 levels to chromosomes 18p11-q12 and 18q12-q21, IgG4 levels to chromosomes 1p31 and 12q24 and IgG levels to chromosome 6p24-p21. Moreover, we genotyped genetic markers located within the regions of interest in a rural population living in Burkina Faso. We detected genome-wide significant and suggestive linkage results when combining the two study populations for chromosomes 1p31, 6p24-p21, 8p22-p21, 9q34, 12q24 and 20q13. Because high anti-parasite IgG3 and low anti-parasite IgG4 levels were associated with malaria resistance, the chromosomal regions linked to IgG3 and IgG4 levels are of special interest. Although the results should be confirmed in an independent population, they may provide new insights in understanding both the genetic control of IgG production and malaria resistance.
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Affiliation(s)
- A Brisebarre
- 1] INSERM, UMR1090 TAGC, Marseille, France [2] Aix-Marseille Université, Marseille, France
| | - B Kumulungui
- Université des Sciences et Techniques de Masuku, Institut National Supérieur d'Agronomie et de Biotechnologies, Franceville, Gabon
| | - S Sawadogo
- University of Ouagadougou, UFR des Sciences de la Santé, Ouagadougou, Burkina Faso
| | - S Afridi
- 1] INSERM, UMR1090 TAGC, Marseille, France [2] Aix-Marseille Université, Marseille, France
| | - F Fumoux
- 1] Aix-Marseille Université, Marseille, France [2] UMR-MD3, Marseille, France
| | - P Rihet
- 1] INSERM, UMR1090 TAGC, Marseille, France [2] Aix-Marseille Université, Marseille, France
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25
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Brisebarre A, Kumulungui B, Sawadogo S, Atkinson A, Garnier S, Fumoux F, Rihet P. A genome scan for Plasmodium falciparum malaria identifies quantitative trait loci on chromosomes 5q31, 6p21.3, 17p12, and 19p13. Malar J 2014; 13:198. [PMID: 24884991 PMCID: PMC4057593 DOI: 10.1186/1475-2875-13-198] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/20/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome-wide studies have mapped several loci controlling Plasmodium falciparum mild malaria and parasitaemia, only two of them being significant at the genome level. The objective of the present study was to identify malaria resistance loci in individuals living in Burkina Faso. METHODS A genome scan that involved 314 individuals belonging to 63 families was performed. Markers located within chromosomes 6p21.3 and 17p12 were genotyped in 247 additional individuals belonging to 55 families. The linkage and the association of markers with parasitaemia and mild malaria were assessed by using the maximum-likelihood binomial method extended to quantitative trait linkage and the quantitative trait disequilibrium test, respectively. RESULTS Multipoint linkage analysis showed a significant linkage of mild malaria to chromosome 6p21.3 (LOD score 3.73, P = 1.7 10-5), a suggestive linkage of mild malaria to chromosome 19p13.12 (LOD score 2.50, P = 3.5 10-4), and a suggestive linkage of asymptomatic parasitaemia to chromosomes 6p21.3 (LOD score 2.36, P = 4.9 10-4) and 17p12 (LOD score 2.87, P = 1.4 10-4). Genome-wide family-based association analysis revealed a significant association between three chromosome 5q31 markers and asymptomatic parasitaemia, whereas there was no association with mild malaria. When taking into account 247 additional individuals, a significant linkage of asymptomatic parasitaemia to chromosome 17p12 (LOD score 3.6, P = 2 10-5) was detected. CONCLUSION A new genome-wide significant malaria locus on chromosome 17p12 and a new suggestive locus on chromosome 19p13.12 are reported. Moreover, there was evidence that confirmed the influence of chromosomes 5q31 and 6p21.3 as loci controlling mild malaria or asymptomatic parasitaemia.
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Affiliation(s)
| | | | | | | | | | | | - Pascal Rihet
- INSERM, UMR1090 TAGC, Marseille F-13288, France.
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26
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Hamidou Soumana I, Tchicaya B, Loriod B, Rihet P, Geiger A. Identification of overexpressed genes in Sodalis glossinidius inhabiting trypanosome-infected self-cured tsetse flies. Front Microbiol 2014; 5:255. [PMID: 24904565 PMCID: PMC4033830 DOI: 10.3389/fmicb.2014.00255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 05/09/2014] [Indexed: 02/03/2023] Open
Abstract
Sodalis glossinidius, one of the three tsetse fly maternally inherited symbionts, was previously shown to favor fly infection by trypanosomes, the parasites causing human sleeping sickness. Among a population of flies taking a trypanosome-infected blood meal, only a few individuals will acquire the parasite; the others will escape infection and be considered as refractory to trypanosome infection. The aim of the work was to investigate whether fly refractoriness could be associated with specific Sodalis gene expression. The transcriptome of S. glossinidius harbored by flies that were fed either with a non-infected blood meal (control) or with a trypanosome-infected meal but that did not develop infection were analyzed, using microarray technology, and compared. The analysis using the microarray procedure yielded 17 genes that were found to have a significant differential expression between the two groups. Interestingly, all these genes were overexpressed in self-cured (refractory) flies. Further analysis of functional annotation of these genes indicated that most associated biological process terms were related to metabolic and biosynthetic processes as well as to oxido-reduction mechanisms. These results evidence the occurrence of molecular crosstalk between the different partners, induced by the passage of the trypanosomes through the fly's gut even though the parasites were unable to establish in the gut and to develop a permanent infection.
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Affiliation(s)
| | | | - Béatrice Loriod
- INSERM, UMR1090 TAGC Marseille, France ; Biology Department, Aix-Marseille University Marseille, France
| | - Pascal Rihet
- INSERM, UMR1090 TAGC Marseille, France ; Biology Department, Aix-Marseille University Marseille, France
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27
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Ramy R, Garnier S, Pradel L, Röder L, Loriod B, Defaye A, Perrin L, Rihet P, Nguyen C. Approaches combining mice and Drosophila melanogaster models to decipher human sepsis. Crit Care 2014. [PMCID: PMC4273906 DOI: 10.1186/cc14070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Hernandez-Valladares M, Rihet P, Iraqi FA. Host susceptibility to malaria in human and mice: compatible approaches to identify potential resistant genes. Physiol Genomics 2014; 46:1-16. [DOI: 10.1152/physiolgenomics.00044.2013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
There is growing evidence for human genetic factors controlling the outcome of malaria infection, while molecular basis of this genetic control is still poorly understood. Case-control and family-based studies have been carried out to identify genes underlying host susceptibility to malarial infection. Parasitemia and mild malaria have been genetically linked to human chromosomes 5q31-q33 and 6p21.3, and several immune genes located within those regions have been associated with malaria-related phenotypes. Association and linkage studies of resistance to malaria are not easy to carry out in human populations, because of the difficulty in surveying a significant number of families. Murine models have proven to be an excellent genetic tool for studying host response to malaria; their use allowed mapping 14 resistance loci, eight of them controlling parasitic levels and six controlling cerebral malaria. Once quantitative trait loci or genes have been identified, the human ortholog may then be identified. Comparative mapping studies showed that a couple of human and mouse might share similar genetically controlled mechanisms of resistance. In this way, char8, which controls parasitemia, was mapped on chromosome 11; char8 corresponds to human chromosome 5q31-q33 and contains immune genes, such as Il3, Il4, Il5, Il12b, Il13, Irf1, and Csf2. Nevertheless, part of the genetic factors controlling malaria traits might differ in both hosts because of specific host-pathogen interactions. Finally, novel genetic tools including animal models were recently developed and will offer new opportunities for identifying genetic factors underlying host phenotypic response to malaria, which will help in better therapeutic strategies including vaccine and drug development.
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Affiliation(s)
| | - Pascal Rihet
- UMR1090 TAGC, INSERM, Marseille, France
- Aix-Marseille University, Marseille, France; and
| | - Fuad A. Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel
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29
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Bouchet A, Sakakini N, El Atifi M, Le Clec'h C, Brauer E, Moisan A, Deman P, Rihet P, Le Duc G, Pelletier L. Early gene expression analysis in 9L orthotopic tumor-bearing rats identifies immune modulation in molecular response to synchrotron microbeam radiation therapy. PLoS One 2013; 8:e81874. [PMID: 24391709 PMCID: PMC3876987 DOI: 10.1371/journal.pone.0081874] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 10/19/2013] [Indexed: 01/21/2023] Open
Abstract
Synchrotron Microbeam Radiation Therapy (MRT) relies on the spatial fractionation of the synchrotron photon beam into parallel micro-beams applying several hundred of grays in their paths. Several works have reported the therapeutic interest of the radiotherapy modality at preclinical level, but biological mechanisms responsible for the described efficacy are not fully understood to date. The aim of this study was to identify the early transcriptomic responses of normal brain and glioma tissue in rats after MRT irradiation (400Gy). The transcriptomic analysis of similarly irradiated normal brain and tumor tissues was performed 6 hours after irradiation of 9 L orthotopically tumor-bearing rats. Pangenomic analysis revealed 1012 overexpressed and 497 repressed genes in the irradiated contralateral normal tissue and 344 induced and 210 repressed genes in tumor tissue. These genes were grouped in a total of 135 canonical pathways. More than half were common to both tissues with a predominance for immunity or inflammation (64 and 67% of genes for normal and tumor tissues, respectively). Several pathways involving HMGB1, toll-like receptors, C-type lectins and CD36 may serve as a link between biochemical changes triggered by irradiation and inflammation and immunological challenge. Most immune cell populations were involved: macrophages, dendritic cells, natural killer, T and B lymphocytes. Among them, our results highlighted the involvement of Th17 cell population, recently described in tumor. The immune response was regulated by a large network of mediators comprising growth factors, cytokines, lymphokines. In conclusion, early response to MRT is mainly based on inflammation and immunity which appear therefore as major contributors to MRT efficacy.
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Affiliation(s)
- Audrey Bouchet
- Institut National de la Santé et de la Recherche Médicale (INSERM) - Unit 836, Team Nanomedecine and brain, La Tronche, France
- European Synchrotron Radiation Facility (ESRF), Biomedical Beamline, Grenoble, France
| | - Nathalie Sakakini
- Unité Mixte de Recherche 1090, Team Technlogical Advances for Genomics and Clinics (TAGC), Institut National de la Santé et de la Recherche Médicale (INSERM), Marseille, France
- Aix-Marseille Université, Marseille, France
| | - Michèle El Atifi
- Institut National de la Santé et de la Recherche Médicale (INSERM) - Unit 836, Team Nanomedecine and brain, La Tronche, France
- Grenoble University Hospital, Grenoble, France
| | - Céline Le Clec'h
- European Synchrotron Radiation Facility (ESRF), Biomedical Beamline, Grenoble, France
| | - Elke Brauer
- European Synchrotron Radiation Facility (ESRF), Biomedical Beamline, Grenoble, France
| | - Anaïck Moisan
- Institut National de la Santé et de la Recherche Médicale (INSERM) - Unit 836, Team Functional NeuroImaging and Brain Perfusion, La Tronche, France
| | - Pierre Deman
- Institut National de la Santé et de la Recherche Médicale (INSERM) - Unit 836, Team Synchrotron Radiation and Medical Research, La Tronche, France
| | - Pascal Rihet
- Unité Mixte de Recherche 1090, Team Technlogical Advances for Genomics and Clinics (TAGC), Institut National de la Santé et de la Recherche Médicale (INSERM), Marseille, France
- Aix-Marseille Université, Marseille, France
| | - Géraldine Le Duc
- European Synchrotron Radiation Facility (ESRF), Biomedical Beamline, Grenoble, France
| | - Laurent Pelletier
- Institut National de la Santé et de la Recherche Médicale (INSERM) - Unit 836, Team Nanomedecine and brain, La Tronche, France
- Grenoble University Hospital, Grenoble, France
- * E-mail:
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Baier C, Fino A, Sanchez C, Farnault L, Rihet P, Kahn-Perlès B, Costello RT. Natural killer cells modulation in hematological malignancies. Front Immunol 2013; 4:459. [PMID: 24391641 PMCID: PMC3867693 DOI: 10.3389/fimmu.2013.00459] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/02/2013] [Indexed: 12/26/2022] Open
Abstract
Hematological malignancies (HM) treatment improved over the last years resulting in increased achievement of complete or partial remission, but unfortunately high relapse rates are still observed, due to remaining minimal residual disease. Therefore, sustainment of long-term remission is crucial, using either drug maintenance treatment or by boosting or prolonging an immune response. Immune system has a key role in tumor surveillance. Nonetheless, tumor-cells evade the specific T-lymphocyte mediated immune surveillance using many mechanisms but especially by the down-regulation of the expression of HLA class I antigens. In theory, these tumor-cells lacking normal expression of HLA class I molecules should be destroyed by natural killer (NK) cells, according to the missing-self hypothesis. NK cells, at the frontier of innate and adaptive immune system, have a central role in tumor-cells surveillance as demonstrated in the setting of allogenic stem cell transplantation. Nevertheless, tumors develop various mechanisms to escape from NK innate immune pressure. Abnormal NK cytolytic functions have been described in many HM. We present here various mechanisms involved in the escape of HM from NK-cell surveillance, i.e., NK-cells quantitative and qualitative abnormalities.
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Affiliation(s)
- Céline Baier
- UMR1090 TAGC, INSERM , Marseille , France ; UMR1090 TAGC, Aix-Marseille Université , Marseille , France
| | - Aurore Fino
- UMR1090 TAGC, INSERM , Marseille , France ; UMR1090 TAGC, Aix-Marseille Université , Marseille , France
| | | | - Laure Farnault
- UMR1090 TAGC, INSERM , Marseille , France ; Service d'hématologie, APHM, Hôpital de la Conception , Marseille , France
| | - Pascal Rihet
- UMR1090 TAGC, INSERM , Marseille , France ; UMR1090 TAGC, Aix-Marseille Université , Marseille , France
| | - Brigitte Kahn-Perlès
- UMR1090 TAGC, INSERM , Marseille , France ; UMR1090 TAGC, Aix-Marseille Université , Marseille , France
| | - Régis T Costello
- UMR1090 TAGC, INSERM , Marseille , France ; UMR1090 TAGC, Aix-Marseille Université , Marseille , France ; Service d'hématologie, APHM, Hôpital de la Conception , Marseille , France
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Lortet S, Lacombe E, Boulanger N, Rihet P, Nguyen C, Kerkerian-Le Goff L, Salin P. Striatal molecular signature of subchronic subthalamic nucleus high frequency stimulation in parkinsonian rat. PLoS One 2013; 8:e60447. [PMID: 23593219 PMCID: PMC3617149 DOI: 10.1371/journal.pone.0060447] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/26/2013] [Indexed: 11/19/2022] Open
Abstract
This study addresses the molecular mechanisms underlying the action of subthalamic nucleus high frequency stimulation (STN-HFS) in the treatment of Parkinson's disease and its interaction with levodopa (L-DOPA), focusing on the striatum. Striatal gene expression profile was assessed in rats with nigral dopamine neuron lesion, either treated or not, using agilent microarrays and qPCR verification. The treatments consisted in anti-akinetic STN-HFS (5 days), chronic L-DOPA treatment inducing dyskinesia (LIDs) or the combination of the two treatments that exacerbated LIDs. STN-HFS modulated 71 striatal genes. The main biological processes associated with the differentially expressed gene products include regulation of growth, of apoptosis and of synaptic transmission, and extracellular region is a major cellular component implicated. In particular, several of these genes have been shown to support survival or differentiation of striatal or of dopaminergic neurons. These results indicate that STN HFS may induce widespread anatomo-functional rearrangements in the striatum and create a molecular environment favorable for neuroprotection and neuroplasticity. STN-HFS and L-DOPA treatment share very few common gene regulation features indicating that the molecular substrates underlying their striatal action are mostly different; among the common effects is the down-regulation of Adrb1, which encodes the adrenergic beta-1-receptor, supporting a major role of this receptor in Parkinson's disease. In addition to genes already reported to be associated with LIDs (preprodynorphin, thyrotropin-releasing hormone, metabotropic glutamate receptor 4, cannabinoid receptor 1), the comparison between DOPA and DOPA/HFS identifies immunity-related genes as potential players in L-DOPA side effects.
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Affiliation(s)
- Sylviane Lortet
- Aix-Marseille Université, CNRS, IBDM UMR 7288, Marseille, France.
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Afridi S, Atkinson A, Garnier S, Fumoux F, Rihet P. Malaria resistance genes are associated with the levels of IgG subclasses directed against Plasmodium falciparum blood-stage antigens in Burkina Faso. Malar J 2012; 11:308. [PMID: 22947458 PMCID: PMC3552815 DOI: 10.1186/1475-2875-11-308] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 08/30/2012] [Indexed: 11/21/2022] Open
Abstract
Background HBB, IL4, IL12, TNF, LTA, NCR3 and FCGR2A polymorphisms have been associated with malaria resistance in humans, whereas cytophilic immunoglobulin G (IgG) antibodies are thought to play a critical role in immune protection against asexual blood stages of the parasite. Furthermore, HBB, IL4, TNF, and FCGR2A have been associated with both malaria resistance and IgG levels. This suggests that some malaria resistance genes influence the levels of IgG subclass antibodies. Methods In this study, the effect of HBB, IL4, IL12, TNF, LTA, NCR3 and FCGR2A polymorphisms on the levels of IgG responses against Plasmodium falciparum blood-stage extract was investigated in 220 individuals living in Burkina Faso. The Pearson’s correlation coefficient among IgG subclasses was determined. A family-based approach was used to assess the association of polymorphisms with anti-P. falciparum IgG, IgG1, IgG2, IgG3 and IgG4 levels. Results After applying a multiple test correction, several polymorphisms were associated with IgG subclass or IgG levels. There was an association of i) haemoglobin C with IgG levels; ii) the FcγRIIa H/R131 with IgG2 and IgG3 levels; iii) TNF-863 with IgG3 levels; iv) TNF-857 with IgG levels; and, v) TNF1304 with IgG3, IgG4, and IgG levels. Conclusion Taken together, the results support the hypothesis that some polymorphisms affect malaria resistance through their effect on the acquired immune response, and pave the way towards further comprehension of genetic control of an individual’s humoral response against malaria.
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Atkinson A, Garnier S, Afridi S, Fumoux F, Rihet P. Genetic variations in genes involved in heparan sulphate biosynthesis are associated with Plasmodium falciparum parasitaemia: a familial study in Burkina Faso. Malar J 2012; 11:108. [PMID: 22475533 PMCID: PMC3364897 DOI: 10.1186/1475-2875-11-108] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 04/04/2012] [Indexed: 12/18/2022] Open
Abstract
Background There is accumulating evidence that host heparan sulphate proteoglycans play an important role in the life cycle of Plasmodium through their heparan sulphate chains, suggesting that genetic variations in genes involved in heparan sulphate biosynthesis may influence parasitaemia. Interestingly, Hs3st3a1 and Hs3st3b1 encoding enzymes involved in the biosynthesis of heparan sulphate are located within a chromosomal region linked to Plasmodium chabaudi parasitaemia in mice. This suggests that HS3ST3A1 and HS3ST3B1 may influence P. falciparum parasitaemia in humans. Methods Polymorphisms within HS3ST3A1 and HS3ST3B1 were identified in 270 individuals belonging to 44 pedigrees and living in Burkina Faso. Linkage and association between parasitaemia and the polymorphisms were assessed with MERLIN and FBAT. A genetic interaction analysis was also conducted based on the PGMDR approach. Results Linkage between P. falciparum parasitaemia and the chromosomal region containing HS3ST3A1 and HS3ST3B1 was detected on the basis of the 20 SNPs identified. In addition, rs28470223 located within the promoter of HS3ST3A1 was associated with P. falciparum parasitaemia, whereas the PGMDR analysis revealed a genetic interaction between HS3ST3A1 and HS3ST3B1. Seventy-three significant multi-locus models were identified after correcting for multiple tests; 37 significant multi-locus models included rs28470223, whereas 38 multi-locus models contained at least one mis-sense mutation within HS3ST3B1. Conclusion Genetic variants of HS3ST3A1 and HS3ST3B1 are associated with P. falciparum parasitaemia. This suggests that those variants alter both the function of heparan sulphate proteoglycans and P. falciparum parasitaemia.
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Fauconnier M, Palomo J, Bourigault ML, Meme S, Szeremeta F, Beloeil JC, Danneels A, Charron S, Rihet P, Ryffel B, Quesniaux VFJ. IL-12Rβ2 Is Essential for the Development of Experimental Cerebral Malaria. J I 2012; 188:1905-14. [DOI: 10.4049/jimmunol.1101978] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Lemaire D, Barbosa T, Rihet P. Coping with genetic diversity: the contribution of pathogen and human genomics to modern vaccinology. Braz J Med Biol Res 2011; 45:376-85. [PMID: 22030866 PMCID: PMC3854287 DOI: 10.1590/s0100-879x2011007500142] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 10/04/2011] [Indexed: 11/21/2022] Open
Abstract
Vaccine development faces major difficulties partly because of genetic variation in both infectious organisms and humans. This causes antigenic variation in infectious agents and a high interindividual variability in the human response to the vaccine. The exponential growth of genome sequence information has induced a shift from conventional culture-based to genome-based vaccinology, and allows the tackling of challenges in vaccine development due to pathogen genetic variability. Additionally, recent advances in immunogenetics and genomics should help in the understanding of the influence of genetic factors on the interindividual and interpopulation variations in immune responses to vaccines, and could be useful for developing new vaccine strategies. Accumulating results provide evidence for the existence of a number of genes involved in protective immune responses that are induced either by natural infections or vaccines. Variation in immune responses could be viewed as the result of a perturbation of gene networks; this should help in understanding how a particular polymorphism or a combination thereof could affect protective immune responses. Here we will present: i) the first genome-based vaccines that served as proof of concept, and that provided new critical insights into vaccine development strategies; ii) an overview of genetic predisposition in infectious diseases and genetic control in responses to vaccines; iii) population genetic differences that are a rationale behind group-targeted vaccines; iv) an outlook for genetic control in infectious diseases, with special emphasis on the concept of molecular networks that will provide a structure to the huge amount of genomic data.
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Affiliation(s)
- D Lemaire
- Universidade Federal da Bahia, Salvador, BA, Brasil
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Barbier M, Faille D, Loriod B, Textoris J, Camus C, Puthier D, Flori L, Wassmer SC, Victorero G, Alessi MC, Fusaï T, Nguyen C, Grau GE, Rihet P. Platelets alter gene expression profile in human brain endothelial cells in an in vitro model of cerebral malaria. PLoS One 2011; 6:e19651. [PMID: 21603600 PMCID: PMC3095604 DOI: 10.1371/journal.pone.0019651] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 04/12/2011] [Indexed: 01/16/2023] Open
Abstract
Platelet adhesion to the brain microvasculature has been associated with cerebral malaria (CM) in humans, suggesting that platelets play a role in the pathogenesis of this syndrome. In vitro co-cultures have shown that platelets can act as a bridge between Plasmodium falciparum-infected red blood cells (pRBC) and human brain microvascular endothelial cells (HBEC) and potentiate HBEC apoptosis. Using cDNA microarray technology, we analyzed transcriptional changes of HBEC in response to platelets in the presence or the absence of tumor necrosis factor (TNF) and pRBC, which have been reported to alter gene expression in endothelial cells. Using a rigorous statistical approach with multiple test corrections, we showed a significant effect of platelets on gene expression in HBEC. We also detected a strong effect of TNF, whereas there was no transcriptional change induced specifically by pRBC. Nevertheless, a global ANOVA and a two-way ANOVA suggested that pRBC acted in interaction with platelets and TNF to alter gene expression in HBEC. The expression of selected genes was validated by RT-qPCR. The analysis of gene functional annotation indicated that platelets induce the expression of genes involved in inflammation and apoptosis, such as genes involved in chemokine-, TREM1-, cytokine-, IL10-, TGFβ-, death-receptor-, and apoptosis-signaling. Overall, our results support the hypothesis that platelets play a pathogenic role in CM.
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Affiliation(s)
- Mathieu Barbier
- Laboratoire de Pharmacogenétique des Maladies Parasitaires-EA 864, IFR 48, Faculté de Pharmacie, Aix-Marseille Université, Marseille, France
| | - Dorothée Faille
- Unité de Recherche en Biologie et en Épidémiologie Parasitaires, UMR 6236-URMITE-IMTSSA, Institut de Recherche Biomédicale des Armées-Antenne Marseille, Marseille, France
- INSERM, UMR 626, Faculté de Médecine, Aix-Marseille Université, Marseille, France
- Vascular Immunology Unit, Department of Pathology, University of Sydney, Camperdown, Australia
| | - Béatrice Loriod
- INSERM U928-TAGC, Aix-Marseille Université, IFR137, Marseille, France
| | - Julien Textoris
- INSERM U928-TAGC, Aix-Marseille Université, IFR137, Marseille, France
| | - Claire Camus
- Laboratoire de Pharmacogenétique des Maladies Parasitaires-EA 864, IFR 48, Faculté de Pharmacie, Aix-Marseille Université, Marseille, France
- INSERM U928-TAGC, Aix-Marseille Université, IFR137, Marseille, France
| | - Denis Puthier
- INSERM U928-TAGC, Aix-Marseille Université, IFR137, Marseille, France
| | - Laurence Flori
- Laboratoire de Génétique Animale et Biologie Intégrative, Domaine de Vilvert, INRA AgroParisTech, Jouy-en-Josas, France
| | - Samuel Crocodile Wassmer
- Department of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
| | | | | | - Thierry Fusaï
- Unité de Recherche en Biologie et en Épidémiologie Parasitaires, UMR 6236-URMITE-IMTSSA, Institut de Recherche Biomédicale des Armées-Antenne Marseille, Marseille, France
| | - Catherine Nguyen
- INSERM U928-TAGC, Aix-Marseille Université, IFR137, Marseille, France
| | - Georges E. Grau
- Vascular Immunology Unit, Department of Pathology, University of Sydney, Camperdown, Australia
| | - Pascal Rihet
- Laboratoire de Pharmacogenétique des Maladies Parasitaires-EA 864, IFR 48, Faculté de Pharmacie, Aix-Marseille Université, Marseille, France
- INSERM U928-TAGC, Aix-Marseille Université, IFR137, Marseille, France
- * E-mail:
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Atkinson A, Barbier M, Afridi S, Fumoux F, Rihet P. Evidence for epistasis between hemoglobin C and immune genes in human P. falciparum malaria: a family study in Burkina Faso. Genes Immun 2011; 12:481-9. [PMID: 21451558 DOI: 10.1038/gene.2011.19] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hemoglobin C (HbC) has been recently associated with protection against Plasmodium falciparum malaria. It is thought that HbC influences the development of immune responses against malaria, suggesting that the variation at the HbC locus (rs33930165) may interact with polymorphic sites in immune genes. We investigated, in 198 individuals belonging to 34 families living in Burkina Faso, statistical interactions between HbC and 11 polymorphisms within interleukin-4 (IL4), IL12B, NCR3, tumor necrosis factor (TNF) and lymphotoxin-α (LTA), which have been previously associated with malaria-related phenotypes. We searched for multilocus interactions by using the pedigree-based generalized multifactor dimensionality reduction approach. We detected 29 multilocus interactions for mild malaria, maximum parasitemia or asymptomatic parasitemia after correcting for multiple tests. All the single-nucleotide polymorphisms studied are included in several multilocus models. Nevertheless, most of the significant multilocus models included IL12B 3' untranslated region, IL12Bpro or LTA+80, suggesting that those polymorphisms play a particular role in the interactions detected. Moreover, we identified six multilocus models involving NCR3 that encodes the activating natural killer (NK) receptor NKp30, suggesting an interaction between HbC and genes involved in the activation of NK cells. More generally, our findings suggest an interaction between HbC and genes influencing the activation of effector cells for phenotypes related to mild malaria.
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Costello R, Sanchez C, Le Treut T, Rihet P, Imbert J, Sébahoun G. Peripheral T-cell lymphoma gene expression profiling and potential therapeutic exploitations. Br J Haematol 2009; 150:21-7. [DOI: 10.1111/j.1365-2141.2009.07977.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Barbier M, Delahaye NF, Fumoux F, Rihet P. Family-based association of a low producing lymphotoxin-alpha allele with reduced Plasmodium falciparum parasitemia. Microbes Infect 2008; 10:673-9. [PMID: 18457972 DOI: 10.1016/j.micinf.2008.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 02/29/2008] [Accepted: 03/13/2008] [Indexed: 11/16/2022]
Abstract
Tumor necrosis factor (TNF)-related genes are thought to play a role in human malaria. TNF polymorphisms have been associated with severe malaria, mild malaria, and parasitemia. Lymphotoxin-alpha gene (LTA) that belongs to the TNF family is one such candidate gene. Here we report the family-based association analysis of a cis-regulatory lymphotoxin-alpha polymorphism with parasitemia in two independent populations living in Burkina Faso. Analysis of 199 subjects (34 families) living in an urban endemic area revealed the association of the low producing LTA+80A allele with reduced parasitemia. Furthermore, there was evidence of significant LTA+80-by-age and LTA+80-by-gender interactions. In another set of 318 residents (55 families) in a rural endemic area, we found both the association of the low producing LTA+80A allele with reduced parasitemia and LTA+80-by-age and LTA+80-by-gender interactions. This study suggests that LTA+80 polymorphism influences parasitemia and acts in an age- and gender-dependent manner.
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Affiliation(s)
- Mathieu Barbier
- Aix-Marseille Université, IFR 48, Faculté de Pharmacie, Laboratoire de Pharmacogénétique des Maladies Parasitaires-EA 864, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
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Rihet P. Innate immunity genes as candidate genes: searching for relevant natural polymorphisms in databases and assessing family-based association of polymorphisms with human diseases. Methods Mol Biol 2008; 415:17-48. [PMID: 18370146 DOI: 10.1007/978-1-59745-570-1_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The identification of genes underlying complex traits is a challenging task, and there are a limited number of confirmed genes that influence human complex diseases. In particular, few genes involved in complex diseases related to immune response, such as infectious diseases and inflammatory diseases, have been identified. Recent advances in genotyping technology lead to the depository of millions of single-nucleotide polymorphisms (SNPs) into public databases, and SNPs are considered powerful tools in the search for genes involved in complex diseases. A number of SNP-genotyping methods are available, and two critical points are to select the SNPs required for a comprehensive analysis and to perform association analyses that avoid statistical biases because of population substructure. This chapter describes a way to take advantage of the mass of known SNPs and to evaluate family-based association between polymorphisms and phenotypes related to diseases, with special emphasis on innate immunity genes. After summarizing relevant aspects of genetic epidemiology, I describe how to obtain SNP data from ENSEMBL visualize an annotated sequence containing SNPs with SNPper select SNPs on the basis of population frequency and functional information explore SNP data in the IIGA database focused on innate immunity genes evaluate the association of SNPs with quantitative phenotypes by using Quantitative trait Transmission/Disequilibrium Tests (QTDT) evaluate the association of SNPs with binary and quantitative phenotypes by using Family-Based Association Tests (FBAT). All the procedures use publicly available servers and free statistical programs for academic users.
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Affiliation(s)
- Pascal Rihet
- Université de la Méditerranée, Marseille Cedex, France
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Delahaye NF, Coltel N, Puthier D, Barbier M, Benech P, Joly F, Iraqi FA, Grau GE, Nguyen C, Rihet P. Gene expression analysis reveals early changes in several molecular pathways in cerebral malaria-susceptible mice versus cerebral malaria-resistant mice. BMC Genomics 2007; 8:452. [PMID: 18062806 PMCID: PMC2246131 DOI: 10.1186/1471-2164-8-452] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Accepted: 12/06/2007] [Indexed: 11/10/2022] Open
Abstract
Background Microarray analyses allow the identification and assessment of molecular signatures in whole tissues undergoing pathological processes. To better understand cerebral malaria pathogenesis, we investigated intra-cerebral gene-expression profiles in well-defined genetically cerebral malaria-resistant (CM-R) and CM-susceptible (CM-S) mice, upon infection by Plasmodium berghei ANKA (PbA). We investigated mouse transcriptional responses at early and late stages of infection by use of cDNA microarrays. Results Through a rigorous statistical approach with multiple testing corrections, we showed that PbA significantly altered brain gene expression in CM-R (BALB/c), and in CM-S (CBA/J and C57BL/6) mice, and that 327 genes discriminated between early and late infection stages, between mouse strains, and between CM-R and CM-S mice. We further identified 104, 56, 84 genes with significant differential expression between CM-R and CM-S mice on days 2, 5, and 7 respectively. The analysis of their functional annotation indicates that genes involved in metabolic energy pathways, the inflammatory response, and the neuroprotection/neurotoxicity balance play a major role in cerebral malaria pathogenesis. In addition, our data suggest that cerebral malaria and Alzheimer's disease may share some common mechanisms of pathogenesis, as illustrated by the accumulation of β-amyloid proteins in brains of CM-S mice, but not of CM-R mice. Conclusion Our microarray analysis highlighted marked changes in several molecular pathways in CM-S compared to CM-R mice, particularly at early stages of infection. This study revealed some promising areas for exploration that may both provide new insight into the knowledge of CM pathogenesis and the development of novel therapeutic strategies.
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Affiliation(s)
- Nicolas F Delahaye
- Laboratoire de Pharmacogénétique des maladies parasitaires-EA864, Université de la Méditerranée, IFR48, Marseille, France.
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Delahaye NF, Barbier M, Fumoux F, Rihet P. Association analyses of NCR3 polymorphisms with P. falciparum mild malaria. Microbes Infect 2007; 9:160-6. [PMID: 17208487 DOI: 10.1016/j.micinf.2006.11.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Revised: 11/01/2006] [Accepted: 11/07/2006] [Indexed: 11/28/2022]
Abstract
Plasmodium falciparum malaria is a major cause of morbidity and mortality in many developing countries especially in sub-Saharan Africa. A susceptibility locus for mild malaria has been mapped to the MHC region, and TNF polymorphisms have been associated with mild malaria. The Natural Cytotoxicity-triggering Receptor 3 (NCR3) gene is located in the peak region of linkage, and is 15kb distal to TNF. In this study, we considered NCR3 as a candidate gene, and we genotyped ten NCR3 single nucleotide polymorphisms (SNPs). Here, we report evidence of an association between mild malaria and NCR3 -412G>C polymorphism located within the promoter. Population-based association analysis showed that NCR3 -412C carriers had more frequent mild malaria attacks than NCR3 -412GG individuals (P=0.001). Using the family-based association test (FBAT) program and its phenotype (PBAT) option, we further found that NCR3 -412C (P=0.0009) and a haplotype containing NCR3 -412C (P=0.008) were significantly associated with increased risk of mild malaria, and that the association was not due to the association of TNF with mild malaria. These observations suggest that there are at least two genes located on the central region of MHC involved in genetic control of human malaria. The association of NCR3 with malaria should provide new insights into the role of Natural Killer cells in this common disease.
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Affiliation(s)
- Nicolas F Delahaye
- Université de la Méditerranée, IFR 48, Faculté de Pharmacie, Laboratoire de Pharmacogénétique des Maladies Parasitaires-EA 864, 27 Bd Jean Moulin 13385 Marseille, France
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Hernandez-Valladares M, Naessens J, Musoke AJ, Sekikawa K, Rihet P, Ole-Moiyoi OK, Busher P, Iraqi FA. Pathology of Tnf-deficient mice infected with Plasmodium chabaudi adami 408XZ. Exp Parasitol 2006; 114:271-8. [PMID: 16716303 DOI: 10.1016/j.exppara.2006.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2006] [Revised: 04/05/2006] [Accepted: 04/06/2006] [Indexed: 10/24/2022]
Abstract
Tumor necrosis factor alpha (Tnf) plays a pleiotropic role in murine malaria. Some investigations have correlated Tnf with hypothermia, hyperlactatemia, hypoglycemia, and a suppression of the erythropoietic response, although others have not. In this study, we have evaluated parasitemia, survival rate and several pathological features in C57BL/6JTnf(-/-) and C57BL/6JTnf(+/+) mice after infection with Plasmodium chabaudi adami 408XZ. Compared to the C57BL/6JTnf(+/+) mice, C57BL/6JTnf(-/-) mice showed increased parasitemia and decreased survival rate, whereas blood glucose, blood lactate and body weight were not significantly different. However, C57BL/6JTnf(-/-) mice suffered significantly more from severe anemia and hypothermia than C57BL/6JTnf(+/+) mice. These results suggest that Tnf is an important mediator of parasite control, but not of anemia development. We hypothesize that the high mortality observed in the Tnf knock-out mice is due to increased anemia and pathology as a direct result of increased levels of parasitemia.
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Affiliation(s)
- M Hernandez-Valladares
- International Livestock Research Institute (ILRI), Naivasha Road, P.O. Box 30709, 00100 Nairobi, Kenya.
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Delahaye NF, Coltel N, Puthier D, Flori L, Houlgatte R, Iraqi FA, Nguyen C, Grau GE, Rihet P. Gene-expression profiling discriminates between cerebral malaria (CM)-susceptible mice and CM-resistant mice. J Infect Dis 2005; 193:312-21. [PMID: 16362897 DOI: 10.1086/498579] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2005] [Accepted: 07/27/2005] [Indexed: 11/04/2022] Open
Abstract
The development of cerebral malaria (CM) in mice with Plasmodium berghei ANKA infection is under genetic control. Brain gene-expression patterns were investigated in well-defined genetically CM-resistant (CM-R; BALB/c and DBA/2) and CM-susceptible (CM-S; C57BL/6 and CBA/J) mice by use of cDNA microarrays. By combining transcriptional profiling with rigorous statistical methods and cluster analysis, we identified a set of 69 genes that perfectly discriminated between mouse strains and between CM-R and CM-S mice. The analysis of gene ontological terms revealed that the genes that clustered and were related to susceptibility to CM preferentially belonged to some biological process classes, such as those pertaining to immune responses. Using a false discovery rate of 5% and the Welch t test, we identified 31 genes with consistent differential expression between CM-R and CM-S mice. These data indicate that microarray analysis may be useful for identification of candidate genes that are potentially responsible for resistance or susceptibility to mouse CM and suggest that candidate genes identified in mice could be specifically tested in humans for an association with disease severity.
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Affiliation(s)
- Nicolas F Delahaye
- Laboratoire de Pharmacogenetique des Maladies Parasitaires-EA864, Universite de la Mediterranee-IFR48, Marseille, France
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Ntoumi F, Flori L, Mayengue PI, Matondo Maya DW, Issifou S, Deloron P, Lell B, Kremsner PG, Rihet P. Influence of Carriage of Hemoglobin AS and the Fcγ Receptor IIa–R131Allele on Levels of Immunoglobulin G2 Antibodies toPlasmodium falciparumMerozoite Antigens in Gabonese Children. J Infect Dis 2005; 192:1975-80. [PMID: 16267770 DOI: 10.1086/497611] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Accepted: 06/16/2005] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND To extend our previous findings showing an imbalanced distribution of immunoglobulin G2 (IgG2) antibodies to Plasmodium falciparum merozoite surface protein 2 (MSP2) and a higher frequency of infection with multiple P. falciparum strains in Gabonese children with sickle cell trait (hemoglobin AS), human Fc gamma receptor (Fc gamma R) IIa (CD32) polymorphism and the rate of in vitro invasion of red blood cells (RBCs) from subjects with either hemoglobin AA or AS by multiple P. falciparum strains were investigated. METHODS Fc gamma RIIa mutation at amino acid position 131 (arginine or histidine) was detected by polymerase chain reaction, and in vitro cultures for parasites were used to assess the invasion rate. RESULTS Fc gamma RIIa polymorphism is normally distributed in this population, with no preferential carriage by children with hemoglobin AS. Lower levels of IgG2 subclass antibodies to MSP2 peptides were independently associated with the Fc gamma RIIa-R131 allele and with carriage of hemoglobin AS. Our data suggest that IgG3 antibody responses to MSP2 epitopes could be exacerbated by lower IgG2 levels in children with hemoglobin AS. CONCLUSIONS The higher rate of invasion of RBCs in the presence of multiple strains may indicate that several invasion pathways are solicited simultaneously, and the longer persistence of ring forms in RBCs from the subjects with hemoglobin AS might reflect a slower multiplication phase, leading to a longer circulation and enhanced phagocytosis of these nonpathogenic parasite forms. This may contribute to the protection against P. falciparum malaria observed in children with hemoglobin AS.
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Affiliation(s)
- Francine Ntoumi
- Unite de Recherches Medicales, Hopital Albert Schweitzer, Lambarene, Gabon.
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Flori L, Delahaye NF, Iraqi FA, Hernandez-Valladares M, Fumoux F, Rihet P. TNF as a malaria candidate gene: polymorphism-screening and family-based association analysis of mild malaria attack and parasitemia in Burkina Faso. Genes Immun 2005; 6:472-80. [PMID: 15931230 DOI: 10.1038/sj.gene.6364231] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We have previously obtained strong evidence for linkage of mild malaria attack to the MHC region, with a peak close to the tumor necrosis factor (TNF) gene. We screened, for polymorphisms, the entire TNF gene in the same sample of 34 families comprising 197 individuals living in a Plasmodium falciparum endemic area and we found 17 polymorphisms. In a longitudinal study, we investigated whether the 11 most frequent and informative polymorphisms were associated with mild malaria attack and maximum parasitemia, which was the highest parasitemia in each individual over 2 years. Mild malaria attack and maximum parasitemia were positively correlated. Transmission disequilibrium tests showed nominal evidence for association between TNF-1031, TNF-308, TNF851 and TNF1304 polymorphisms, and mild malaria attack on the one hand, and between TNF-238, TNF851 and TNF1304 polymorphisms, and maximum parasitemia on the other hand. After accounting for multiple tests, we confirmed the association of TNF-238 with maximum parasitemia and the association of TNF1304 and TNF851 with maximum parasitemia and mild malaria attack. The association tests with mild malaria attack suggest a moderate effect of TNF-308 polymorphism. In conclusion, our study suggests that several TNF variants may be part of the genetic determinants for maximum parasitemia and/or mild malaria attack.
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Affiliation(s)
- L Flori
- Laboratoire d'immunogénétique et de pharmacologie du paludisme-EA 864, Faculté de Pharmacie, Université de la Méditerranée, IFR 48, Marseille Cedex, France
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Hernandez-Valladares M, Naessens J, Nagda S, Musoke AJ, Rihet P, Ole-Moiyoi OK, Iraqi FA. Comparison of pathology in susceptible A/J and resistant C57BL/6J mice after infection with different sub-strains of Plasmodium chabaudi. Exp Parasitol 2005; 108:134-41. [PMID: 15582510 DOI: 10.1016/j.exppara.2004.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2004] [Revised: 04/08/2004] [Accepted: 07/27/2004] [Indexed: 11/29/2022]
Abstract
Susceptible A/J and more resistant C57BL/6J mice were infected with Plasmodium chabaudi chabaudi 54X, P.c. chabaudi AS and Plasmodium chabaudi adami 408XZ. As expected, most C57BL/6J mice survived the infections with the different isolates. But in contrast to previous observations, not all A/J mice succumbed to infection: just over 50% of A/J mice survived infections with P.c. chabaudi 54X, while 80% survived P.c. chabaudi AS. The more virulent parasite, P.c. adami 408XZ, was able to kill all A/J mice and 20% of C57BL/6J mice after an intravenous infection with 10(5) pRBC. A detailed study of four parameters of pathology (body weight, body temperature, blood glucose and RBC counts) in both mouse strains after a P.c. adami 408XZ infection showed similar patterns to those previously reported after infection with P.c. chabaudi AS. These data suggest that environmental factors as well as parasite polymorphisms might influence the severity of malaria between susceptible and resistant mice.
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Affiliation(s)
- M Hernandez-Valladares
- International Livestock Research Institute , Naivasha Road, P.O. Box 30709, 00100 Nairobi, Kenya
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Hernandez-Valladares M, Naessens J, Gibson JP, Musoke AJ, Nagda S, Rihet P, Ole-MoiYoi OK, Iraqi FA. Confirmation and dissection of QTL controlling resistance to malaria in mice. Mamm Genome 2004; 15:390-8. [PMID: 15170228 DOI: 10.1007/s00335-004-3042-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2003] [Accepted: 12/17/2003] [Indexed: 11/25/2022]
Abstract
We developed an F(11) AIL population from an F(1) cross of A/J (susceptible) and C57BL/6J (resistant) mouse strains. One thousand F(11) mice were challenged with P.c. chabaudi 54X, and 340 mice selected from the phenotypic extremes for susceptibility and resistance were genotyped for microsatellite markers on Chromosomes (Chrs) 5, 8, and 17. QTL originally detected in backcross and F(2) populations were confirmed on the three chromosomes within narrower genomic regions, by maximum likelihood and regression analyses. Each of the previously mapped QTL on Chrs 5 and 17 resolved into two linked QTLs. The distal and proximal QTLs on Chrs 5 and 17, respectively, map to the previously reported QTL.
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Hernandez-Valladares M, Rihet P, ole-MoiYoi OK, Iraqi FA. Mapping of a new quantitative trait locus for resistance to malaria in mice by a comparative mapping approach with human Chromosome 5q31-q33. Immunogenetics 2004; 56:115-7. [PMID: 15118851 DOI: 10.1007/s00251-004-0667-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2003] [Revised: 03/08/2004] [Indexed: 10/26/2022]
Abstract
A number of linkage studies in human populations have identified a locus ( pfbi) on Chromosome 5q31-q33 controlling Plasmodiun falciparum blood infection levels. This region contains numerous candidate genes encoding immunological molecules such as cytokines, growth factors and growth-factor receptors. We have used an F(11) advance intercross line (AIL) population of mice infected with Plasmodium chabaudi to identify additional mouse quantitative trait loci (QTL) for control of parasitaemia on Chrs 11 and 18, which carry regions homologous to human Chr 5q31-q33. Herein, we report a novel QTL for parasitaemia control ( char8) on the mouse Chr 11, linked to marker D11Mit242, and involved in the clearance stages of the parasites from the bloodstream. Strikingly, several Th2 cytokines that are located within char8 have been identified to play a predominant role in the late stages of the infection.
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Rihet P, Flori L, Tall F, Traore AS, Fumoux F. Hemoglobin C is associated with reduced Plasmodium falciparum parasitemia and low risk of mild malaria attack. Hum Mol Genet 2003; 13:1-6. [PMID: 14613965 DOI: 10.1093/hmg/ddh002] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genetic predisposition to malaria has been shown by epidemiological, case-control and linkage studies. In particular, case-control studies have recently shown association between hemoglobin C and resistance to severe malaria in Mali and to clinical malaria in Burkina Faso. In a longitudinal study of families living in an endemic area, we investigated whether hemoglobin C is associated with reduced Plasmodium falciparum parasitemia and low risk of mild malaria attack. We surveyed 256 individuals (71 parents and 185 sibs) from 53 families during 2 years. Hemoglobin C carriers had less frequent malaria attacks than AA individuals within the same age group (P=0.01). Since age correlated with malaria attack and parasitemia (P<0.0001), we took age into account in association analyses. We performed combined linkage and association analyses, which avoid biases due to population structure. Using multi-allelic tests, we evidenced association between hemoglobin genotype and phenotypes related to malarial infection and disease (P<0.001). We further analyzed individual hemoglobin alleles and detected negative association between hemoglobin C and malaria attack (P=0.00013). Analyses that took into account confounding factors confirmed the negative association of hemoglobin C with malaria attack (P=0.0074) and evidenced a negative correlation between hemoglobin C and parasitemia (P=0.0009). These associations indicate that hemoglobin C reduces parasitemia and confers protection against mild malaria attack.
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Affiliation(s)
- Pascal Rihet
- Université de la Méditerranée, IFR48, Faculté de Pharmacie, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France.
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