20 results on '"Seyres D"'
Search Results
2. Genes and networks regulating cardiac development and function in flies: genetic and functional genomic approaches
- Author
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Seyres, D., primary, Roder, L., additional, and Perrin, L., additional
- Published
- 2012
- Full Text
- View/download PDF
3. Platelet function is modified by common sequence variation in megakaryocyte super enhancers
- Author
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Petersen, R, Lambourne, JJ, Javierre, BM, Grassi, L, Kreuzhuber, R, Ruklisa, D, Rosa, IM, Tomé, AR, Elding, H, Van Geffen, JP, Jiang, T, Farrow, S, Cairns, J, Al-Subaie, AM, Ashford, S, Attwood, A, Batista, J, Bouman, H, Burden, F, Choudry, FA, Clarke, L, Flicek, P, Garner, SF, Haimel, M, Kempster, C, Ladopoulos, V, Lenaerts, A-S, Materek, PM, McKinney, H, Meacham, S, Mead, D, Nagy, M, Penkett, CJ, Rendon, A, Seyres, D, Sun, B, Tuna, S, Van Der Weide, M-E, Wingett, SW, Martens, JH, Stegle, O, Richardson, S, Vallier, L, Roberts, DJ, Freson, K, Wernisch, L, Stunnenberg, HG, Danesh, J, Fraser, P, Soranzo, N, Butterworth, AS, Heemskerk, JW, Turro, E, Spivakov, M, Ouwehand, WH, Astle, WJ, Downes, K, Kostadima, M, and Frontini, M
- Subjects
Blood Platelets ,Enhancer Elements, Genetic ,Erythroblasts ,Genetic Variation ,Humans ,Promoter Regions, Genetic ,Megakaryocytes ,Chromatin ,3. Good health - Abstract
Linking non-coding genetic variants associated with the risk of diseases or disease-relevant traits to target genes is a crucial step to realize GWAS potential in the introduction of precision medicine. Here we set out to determine the mechanisms underpinning variant association with platelet quantitative traits using cell type-matched epigenomic data and promoter long-range interactions. We identify potential regulatory functions for 423 of 565 (75%) non-coding variants associated with platelet traits and we demonstrate, through ex vivo and proof of principle genome editing validation, that variants in super enhancers play an important role in controlling archetypical platelet functions.
4. Selective haematological cancer eradication with preserved haematopoiesis.
- Author
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Garaudé S, Marone R, Lepore R, Devaux A, Beerlage A, Seyres D, Dell' Aglio A, Juskevicius D, Zuin J, Burgold T, Wang S, Katta V, Manquen G, Li Y, Larrue C, Camus A, Durzynska I, Wellinger LC, Kirby I, Van Berkel PH, Kunz C, Tamburini J, Bertoni F, Widmer CC, Tsai SQ, Simonetta F, Urlinger S, and Jeker LT
- Subjects
- Animals, Female, Humans, Male, Mice, Hematopoietic Stem Cell Transplantation, Hematopoietic Stem Cells cytology, Hematopoietic Stem Cells drug effects, Hematopoietic Stem Cells metabolism, Cell Line, Tumor, Antibody Specificity, Hematologic Neoplasms drug therapy, Hematologic Neoplasms therapy, Hematologic Neoplasms immunology, Hematopoiesis drug effects, Immunoconjugates pharmacology, Immunoconjugates therapeutic use, Leukocyte Common Antigens immunology, Leukocyte Common Antigens metabolism
- Abstract
Haematopoietic stem cell (HSC) transplantation (HSCT) is the only curative treatment for a broad range of haematological malignancies, but the standard of care relies on untargeted chemotherapies and limited possibilities to treat malignant cells after HSCT without affecting the transplanted healthy cells
1 . Antigen-specific cell-depleting therapies hold the promise of much more targeted elimination of diseased cells, as witnessed in the past decade by the revolution of clinical practice for B cell malignancies2 . However, target selection is complex and limited to antigens expressed on subsets of haematopoietic cells, resulting in a fragmented therapy landscape with high development costs2-5 . Here we demonstrate that an antibody-drug conjugate (ADC) targeting the pan-haematopoietic marker CD45 enables the antigen-specific depletion of the entire haematopoietic system, including HSCs. Pairing this ADC with the transplantation of human HSCs engineered to be shielded from the CD45-targeting ADC enables the selective eradication of leukaemic cells with preserved haematopoiesis. The combination of CD45-targeting ADCs and engineered HSCs creates an almost universal strategy to replace a diseased haematopoietic system, irrespective of disease aetiology or originating cell type. We propose that this approach could have broad implications beyond haematological malignancies., (© 2024. The Author(s).)- Published
- 2024
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5. T helper cells exhibit a dynamic and reversible 3'-UTR landscape.
- Author
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Seyres D, Gorka O, Schmidt R, Marone R, Zavolan M, and Jeker LT
- Subjects
- 3' Untranslated Regions, RNA-Seq, RNA, Messenger metabolism, T-Lymphocytes, Helper-Inducer metabolism, RNA-Binding Proteins genetics, RNA-Binding Proteins metabolism, Polyadenylation, MicroRNAs genetics, MicroRNAs metabolism
- Abstract
3' untranslated regions (3' UTRs) are critical elements of messenger RNAs, as they contain binding sites for RNA-binding proteins (RBPs) and microRNAs that affect various aspects of the RNA life cycle including transcript stability and cellular localization. In response to T cell receptor activation, T cells undergo massive expansion during the effector phase of the immune response and dynamically modify their 3' UTRs. Whether this serves to directly regulate the abundance of specific mRNAs or is a secondary effect of proliferation remains unclear. To study 3'-UTR dynamics in T helper cells, we investigated division-dependent alternative polyadenylation (APA). In addition, we generated 3' end UTR sequencing data from naive, activated, memory, and regulatory CD4
+ T cells. 3'-UTR length changes were estimated using a nonnegative matrix factorization approach and were compared with those inferred from long-read PacBio sequencing. We found that APA events were transient and reverted after effector phase expansion. Using an orthogonal bulk RNA-seq data set, we did not find evidence of APA association with differential gene expression or transcript usage, indicating that APA has only a marginal effect on transcript abundance. 3'-UTR sequence analysis revealed conserved binding sites for T cell-relevant microRNAs and RBPs in the alternative 3' UTRs. These results indicate that poly(A) site usage could play an important role in the control of cell fate decisions and homeostasis., (© 2024 Seyres et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.)- Published
- 2024
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6. Epitope-engineered human hematopoietic stem cells are shielded from CD123-targeted immunotherapy.
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Marone R, Landmann E, Devaux A, Lepore R, Seyres D, Zuin J, Burgold T, Engdahl C, Capoferri G, Dell'Aglio A, Larrue C, Simonetta F, Rositzka J, Rhiel M, Andrieux G, Gallagher DN, Schröder MS, Wiederkehr A, Sinopoli A, Do Sacramento V, Haydn A, Garcia-Prat L, Divsalar C, Camus A, Xu L, Bordoli L, Schwede T, Porteus M, Tamburini J, Corn JE, Cathomen T, Cornu TI, Urlinger S, and Jeker LT
- Subjects
- Humans, Epitopes, Immunotherapy, Hematopoietic Stem Cells metabolism, Immunotherapy, Adoptive, Interleukin-3 Receptor alpha Subunit metabolism, Leukemia, Myeloid, Acute genetics, Leukemia, Myeloid, Acute therapy
- Abstract
Targeted eradication of transformed or otherwise dysregulated cells using monoclonal antibodies (mAb), antibody-drug conjugates (ADC), T cell engagers (TCE), or chimeric antigen receptor (CAR) cells is very effective for hematologic diseases. Unlike the breakthrough progress achieved for B cell malignancies, there is a pressing need to find suitable antigens for myeloid malignancies. CD123, the interleukin-3 (IL-3) receptor alpha-chain, is highly expressed in various hematological malignancies, including acute myeloid leukemia (AML). However, shared CD123 expression on healthy hematopoietic stem and progenitor cells (HSPCs) bears the risk for myelotoxicity. We demonstrate that epitope-engineered HSPCs were shielded from CD123-targeted immunotherapy but remained functional, while CD123-deficient HSPCs displayed a competitive disadvantage. Transplantation of genome-edited HSPCs could enable tumor-selective targeted immunotherapy while rebuilding a fully functional hematopoietic system. We envision that this approach is broadly applicable to other targets and cells, could render hitherto undruggable targets accessible to immunotherapy, and will allow continued posttransplant therapy, for instance, to treat minimal residual disease (MRD)., (© 2023 Marone et al.)
- Published
- 2023
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7. A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology.
- Author
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Akbari P, Vuckovic D, Stefanucci L, Jiang T, Kundu K, Kreuzhuber R, Bao EL, Collins JH, Downes K, Grassi L, Guerrero JA, Kaptoge S, Knight JC, Meacham S, Sambrook J, Seyres D, Stegle O, Verboon JM, Walter K, Watkins NA, Danesh J, Roberts DJ, Di Angelantonio E, Sankaran VG, Frontini M, Burgess S, Kuijpers T, Peters JE, Butterworth AS, Ouwehand WH, Soranzo N, and Astle WJ
- Subjects
- Microscopy, Transcription Factors, Causality, Genome-Wide Association Study, Proteomics
- Abstract
Blood cells contain functionally important intracellular structures, such as granules, critical to immunity and thrombosis. Quantitative variation in these structures has not been subjected previously to large-scale genetic analysis. We perform genome-wide association studies of 63 flow-cytometry derived cellular phenotypes-including cell-type specific measures of granularity, nucleic acid content and reactivity-in 41,515 participants in the INTERVAL study. We identify 2172 distinct variant-trait associations, including associations near genes coding for proteins in organelles implicated in inflammatory and thrombotic diseases. By integrating with epigenetic data we show that many intracellular structures are likely to be determined in immature precursor cells. By integrating with proteomic data we identify the transcription factor FOG2 as an early regulator of platelet formation and α-granularity. Finally, we show that colocalisation of our associations with disease risk signals can suggest aetiological cell-types-variants in IL2RA and ITGA4 respectively mirror the known effects of daclizumab in multiple sclerosis and vedolizumab in inflammatory bowel disease., (© 2023. Springer Nature Limited.)
- Published
- 2023
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8. Forced expression of the non-coding RNA miR-17∼92 restores activation and function in CD28-deficient CD4 + T cells.
- Author
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Dölz M, Hasiuk M, Gagnon JD, Kornete M, Marone R, Bantug G, Kageyama R, Hess C, Ansel KM, Seyres D, Roux J, and Jeker LT
- Abstract
CD28 provides the prototypical costimulatory signal required for productive T-cell activation. Known molecular consequences of CD28 costimulation are mostly based on studies of protein signaling molecules. The microRNA cluster miR-17∼92 is induced by T cell receptor stimulation and further enhanced by combined CD28 costimulation. We demonstrate that transgenic miR-17∼92 cell-intrinsically largely overcomes defects caused by CD28 deficiency. Combining genetics, transcriptomics, bioinformatics, and biochemical miRNA:mRNA interaction maps we empirically validate miR-17∼92 target genes that include several negative regulators of T cell activation. CD28-deficient T cells exhibit derepressed miR-17∼92 target genes during activation. CRISPR/Cas9-mediated ablation of the miR-17∼92 targets Pten and Nrbp1 in naive CD28
-/- CD4+ T cells differentially increases proliferation and expression of the activation markers CD25 and CD44, respectively. Thus, we propose that miR-17∼92 constitutes a central mediator for T cell activation, integrating signals by the TCR and CD28 costimulation by dampening multiple brakes that prevent T cell activation., Competing Interests: L.T.J. is a co-founder and board member of, holds equity in, and has a sponsored research agreement with Cimeio Therapeutics AG. M.D. and L.T.J. are inventors on a patent application related to the findings reported here., (© 2022 The Author(s).)- Published
- 2022
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9. Transcriptional, epigenetic and metabolic signatures in cardiometabolic syndrome defined by extreme phenotypes.
- Author
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Seyres D, Cabassi A, Lambourne JJ, Burden F, Farrow S, McKinney H, Batista J, Kempster C, Pietzner M, Slingsby O, Cao TH, Quinn PA, Stefanucci L, Sims MC, Rehnstrom K, Adams CL, Frary A, Ergüener B, Kreuzhuber R, Mocciaro G, D'Amore S, Koulman A, Grassi L, Griffin JL, Ng LL, Park A, Savage DB, Langenberg C, Bock C, Downes K, Wareham NJ, Allison M, Vacca M, Kirk PDW, and Frontini M
- Subjects
- DNA Methylation, Epigenesis, Genetic, Humans, Phenotype, Lipodystrophy, Metabolic Syndrome genetics, Obesity, Morbid surgery
- Abstract
Background: This work is aimed at improving the understanding of cardiometabolic syndrome pathophysiology and its relationship with thrombosis by generating a multi-omic disease signature., Methods/results: We combined classic plasma biochemistry and plasma biomarkers with the transcriptional and epigenetic characterisation of cell types involved in thrombosis, obtained from two extreme phenotype groups (morbidly obese and lipodystrophy) and lean individuals to identify the molecular mechanisms at play, highlighting patterns of abnormal activation in innate immune phagocytic cells. Our analyses showed that extreme phenotype groups could be distinguished from lean individuals, and from each other, across all data layers. The characterisation of the same obese group, 6 months after bariatric surgery, revealed the loss of the abnormal activation of innate immune cells previously observed. However, rather than reverting to the gene expression landscape of lean individuals, this occurred via the establishment of novel gene expression landscapes. NETosis and its control mechanisms emerge amongst the pathways that show an improvement after surgical intervention., Conclusions: We showed that the morbidly obese and lipodystrophy groups, despite some differences, shared a common cardiometabolic syndrome signature. We also showed that this could be used to discriminate, amongst the normal population, those individuals with a higher likelihood of presenting with the disease, even when not displaying the classic features., (© 2022. The Author(s).)
- Published
- 2022
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10. Cell type-specific novel long non-coding RNA and circular RNA in the BLUEPRINT hematopoietic transcriptomes atlas.
- Author
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Grassi L, Izuogu OG, Jorge NAN, Seyres D, Bustamante M, Burden F, Farrow S, Farahi N, Martin FJ, Frankish A, Mudge JM, Kostadima M, Petersen R, Lambourne JJ, Rowlston S, Martin-Rendon E, Clarke L, Downes K, Estivill X, Flicek P, Martens JHA, Yaspo ML, Stunnenberg HG, Ouwehand WH, Passetti F, Turro E, and Frontini M
- Subjects
- Gene Expression Profiling, High-Throughput Nucleotide Sequencing, RNA, Circular, Sequence Analysis, RNA, RNA, Long Noncoding genetics, Transcriptome
- Abstract
Transcriptional profiling of hematopoietic cell subpopulations has helped to characterize the developmental stages of the hematopoietic system and the molecular bases of malignant and non-malignant blood diseases. Previously, only the genes targeted by expression microarrays could be profiled genome-wide. High-throughput RNA sequencing, however, encompasses a broader repertoire of RNA molecules, without restriction to previously annotated genes. We analyzed the BLUEPRINT consortium RNA-sequencing data for mature hematopoietic cell types. The data comprised 90 total RNA-sequencing samples, each composed of one of 27 cell types, and 32 small RNA-sequencing samples, each composed of one of 11 cell types. We estimated gene and isoform expression levels for each cell type using existing annotations from Ensembl. We then used guided transcriptome assembly to discover unannotated transcripts. We identified hundreds of novel non-coding RNA genes and showed that the majority have cell type-dependent expression. We also characterized the expression of circular RNA and found that these are also cell type-specific. These analyses refine the active transcriptional landscape of mature hematopoietic cells, highlight abundant genes and transcriptional isoforms for each blood cell type, and provide a valuable resource for researchers of hematologic development and diseases. Finally, we made the data accessible via a web-based interface: https://blueprint.haem.cam.ac.uk/bloodatlas/.
- Published
- 2021
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11. Novel manifestations of immune dysregulation and granule defects in gray platelet syndrome.
- Author
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Sims MC, Mayer L, Collins JH, Bariana TK, Megy K, Lavenu-Bombled C, Seyres D, Kollipara L, Burden FS, Greene D, Lee D, Rodriguez-Romera A, Alessi MC, Astle WJ, Bahou WF, Bury L, Chalmers E, Da Silva R, De Candia E, Deevi SVV, Farrow S, Gomez K, Grassi L, Greinacher A, Gresele P, Hart D, Hurtaud MF, Kelly AM, Kerr R, Le Quellec S, Leblanc T, Leinøe EB, Mapeta R, McKinney H, Michelson AD, Morais S, Nugent D, Papadia S, Park SJ, Pasi J, Podda GM, Poon MC, Reed R, Sekhar M, Shalev H, Sivapalaratnam S, Steinberg-Shemer O, Stephens JC, Tait RC, Turro E, Wu JKM, Zieger B, Kuijpers TW, Whetton AD, Sickmann A, Freson K, Downes K, Erber WN, Frontini M, Nurden P, Ouwehand WH, Favier R, and Guerrero JA
- Subjects
- Biopsy, Blood Proteins genetics, Case-Control Studies, Cohort Studies, Cytoplasmic Granules metabolism, Diagnosis, Differential, Gene Frequency, Genetic Association Studies, Humans, Immune System physiology, Immune System Diseases blood, Immune System Diseases diagnosis, Immune System Diseases genetics, Immune System Diseases pathology, Mutation, Cytoplasmic Granules pathology, Genetic Heterogeneity, Gray Platelet Syndrome classification, Gray Platelet Syndrome genetics, Gray Platelet Syndrome immunology, Gray Platelet Syndrome pathology, Immune System pathology, Phenotype
- Abstract
Gray platelet syndrome (GPS) is a rare recessive disorder caused by biallelic variants in NBEAL2 and characterized by bleeding symptoms, the absence of platelet α-granules, splenomegaly, and bone marrow (BM) fibrosis. Due to the rarity of GPS, it has been difficult to fully understand the pathogenic processes that lead to these clinical sequelae. To discern the spectrum of pathologic features, we performed a detailed clinical genotypic and phenotypic study of 47 patients with GPS and identified 32 new etiologic variants in NBEAL2. The GPS patient cohort exhibited known phenotypes, including macrothrombocytopenia, BM fibrosis, megakaryocyte emperipolesis of neutrophils, splenomegaly, and elevated serum vitamin B12 levels. Novel clinical phenotypes were also observed, including reduced leukocyte counts and increased presence of autoimmune disease and positive autoantibodies. There were widespread differences in the transcriptome and proteome of GPS platelets, neutrophils, monocytes, and CD4 lymphocytes. Proteins less abundant in these cells were enriched for constituents of granules, supporting a role for Nbeal2 in the function of these organelles across a wide range of blood cells. Proteomic analysis of GPS plasma showed increased levels of proteins associated with inflammation and immune response. One-quarter of plasma proteins increased in GPS are known to be synthesized outside of hematopoietic cells, predominantly in the liver. In summary, our data show that, in addition to the well-described platelet defects in GPS, there are immune defects. The abnormal immune cells may be the drivers of systemic abnormalities such as autoimmune disease., (© 2020 by The American Society of Hematology.)
- Published
- 2020
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12. Germline mutations in the transcription factor IKZF5 cause thrombocytopenia.
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Lentaigne C, Greene D, Sivapalaratnam S, Favier R, Seyres D, Thys C, Grassi L, Mangles S, Sibson K, Stubbs M, Burden F, Bordet JC, Armari-Alla C, Erber W, Farrow S, Gleadall N, Gomez K, Megy K, Papadia S, Penkett CJ, Sims MC, Stefanucci L, Stephens JC, Read RJ, Stirrups KE, Ouwehand WH, Laffan MA, Frontini M, Freson K, and Turro E
- Subjects
- Chromatin genetics, Chromatin metabolism, Chromatin ultrastructure, Cytoplasmic Granules genetics, Cytoplasmic Granules metabolism, Cytoplasmic Granules ultrastructure, Female, Gene Expression Regulation, HEK293 Cells, Humans, Male, Blood Platelets metabolism, Blood Platelets ultrastructure, Genetic Diseases, Inborn genetics, Genetic Diseases, Inborn metabolism, Genetic Diseases, Inborn pathology, Germ-Line Mutation, Ikaros Transcription Factor genetics, Ikaros Transcription Factor metabolism, Mutation, Missense, Thrombocytopenia genetics, Thrombocytopenia metabolism, Thrombocytopenia pathology, Thrombopoiesis genetics
- Abstract
To identify novel causes of hereditary thrombocytopenia, we performed a genetic association analysis of whole-genome sequencing data from 13 037 individuals enrolled in the National Institute for Health Research (NIHR) BioResource, including 233 cases with isolated thrombocytopenia. We found an association between rare variants in the transcription factor-encoding gene IKZF5 and thrombocytopenia. We report 5 causal missense variants in or near IKZF5 zinc fingers, of which 2 occurred de novo and 3 co-segregated in 3 pedigrees. A canonical DNA-zinc finger binding model predicts that 3 of the variants alter DNA recognition. Expression studies showed that chromatin binding was disrupted in mutant compared with wild-type IKZF5, and electron microscopy revealed a reduced quantity of α granules in normally sized platelets. Proplatelet formation was reduced in megakaryocytes from 7 cases relative to 6 controls. Comparison of RNA-sequencing data from platelets, monocytes, neutrophils, and CD4+ T cells from 3 cases and 14 healthy controls showed 1194 differentially expressed genes in platelets but only 4 differentially expressed genes in each of the other blood cell types. In conclusion, IKZF5 is a novel transcriptional regulator of megakaryopoiesis and the eighth transcription factor associated with dominant thrombocytopenia in humans., (© 2019 by The American Society of Hematology.)
- Published
- 2019
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13. Sphingolipid dysregulation due to lack of functional KDSR impairs proplatelet formation causing thrombocytopenia.
- Author
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Bariana TK, Labarque V, Heremans J, Thys C, De Reys M, Greene D, Jenkins B, Grassi L, Seyres D, Burden F, Whitehorn D, Shamardina O, Papadia S, Gomez K, BioResource N, Van Geet C, Koulman A, Ouwehand WH, Ghevaert C, Frontini M, Turro E, and Freson K
- Subjects
- Alcohol Oxidoreductases genetics, Animals, Blood Platelets metabolism, Cell Differentiation, Cells, Cultured, Child, Female, Humans, Induced Pluripotent Stem Cells metabolism, Male, Megakaryocytes metabolism, Metabolomics, Mutation, Pedigree, Prognosis, Thrombocytopenia metabolism, Thrombocytopenia pathology, Zebrafish, Alcohol Oxidoreductases deficiency, Blood Platelets pathology, Induced Pluripotent Stem Cells pathology, Megakaryocytes pathology, Sphingolipids metabolism, Thrombocytopenia etiology
- Abstract
Sphingolipids are fundamental to membrane trafficking, apoptosis, and cell differentiation and proliferation. KDSR or 3-keto-dihydrosphingosine reductase is an essential enzyme for de novo sphingolipid synthesis, and pathogenic mutations in KDSR result in the severe skin disorder erythrokeratodermia variabilis et progressiva-4 Four of the eight reported cases also had thrombocytopenia but the underlying mechanism has remained unexplored. Here we expand upon the phenotypic spectrum of KDSR deficiency with studies in two siblings with novel compound heterozygous variants associated with thrombocytopenia, anemia, and minimal skin involvement. We report a novel phenotype of progressive juvenile myelofibrosis in the propositus, with spontaneous recovery of anemia and thrombocytopenia in the first decade of life. Examination of bone marrow biopsies showed megakaryocyte hyperproliferation and dysplasia. Megakaryocytes obtained by culture of CD34
+ stem cells confirmed hyperproliferation and showed reduced proplatelet formation. The effect of KDSR insufficiency on the sphingolipid profile was unknown, and was explored in vivo and in vitro by a broad metabolomics screen that indicated activation of an in vivo compensatory pathway that leads to normalization of downstream metabolites such as ceramide. Differentiation of propositus-derived induced pluripotent stem cells to megakaryocytes followed by expression of functional KDSR showed correction of the aberrant cellular and biochemical phenotypes, corroborating the critical role of KDSR in proplatelet formation. Finally, Kdsr depletion in zebrafish recapitulated the thrombocytopenia and showed biochemical changes similar to those observed in the affected siblings. These studies support an important role for sphingolipids as regulators of cytoskeletal organization during megakaryopoiesis and proplatelet formation., (Copyright© 2019 Ferrata Storti Foundation.)- Published
- 2019
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14. Histone Acetyltransferase KAT2A Stabilizes Pluripotency with Control of Transcriptional Heterogeneity.
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Moris N, Edri S, Seyres D, Kulkarni R, Domingues AF, Balayo T, Frontini M, and Pina C
- Subjects
- Animals, Cell Differentiation, Genetic Heterogeneity, Humans, Mice, Pluripotent Stem Cells cytology, Pluripotent Stem Cells metabolism, Histone Acetyltransferases genetics, Histone Acetyltransferases metabolism, Pluripotent Stem Cells physiology
- Abstract
Cell fate transitions in mammalian stem cell systems have often been associated with transcriptional heterogeneity; however, existing data have failed to establish a functional or mechanistic link between the two phenomena. Experiments in unicellular organisms support the notion that transcriptional heterogeneity can be used to facilitate adaptability to environmental changes and have identified conserved chromatin-associated factors that modulate levels of transcriptional noise. Herein, we show destabilization of pluripotency-associated gene regulatory networks through increased transcriptional heterogeneity of mouse embryonic stem cells in which paradigmatic histone acetyl-transferase, and candidate noise modulator, Kat2a (yeast orthologue Gcn5), have been inhibited. Functionally, network destabilization associates with reduced pluripotency and accelerated mesendodermal differentiation, with increased probability of transitions into lineage commitment. Thus, we show evidence of a relationship between transcriptional heterogeneity and cell fate transitions through manipulation of the histone acetylation landscape of mouse embryonic stem cells, suggesting a general principle that could be exploited in other normal and malignant stem cell fate transitions. Stem Cells 2018;36:1828-11., (©2018 The Authors Stem Cells published by Wiley Periodicals, Inc. on behalf of AlphaMed Press 2018.)
- Published
- 2018
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15. Interplay between trauma and Pseudomonas entomophila infection in flies: a central role of the JNK pathway and of CrebA.
- Author
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Ragheb R, Chuyen A, Torres M, Defaye A, Seyres D, Kremmer L, Fernandez-Nunez N, Tricoire H, Rihet P, Nguyen C, Röder L, and Perrin L
- Subjects
- Animals, Drosophila melanogaster, Signal Transduction, Transcriptome, Wounds and Injuries microbiology, Cyclic AMP Response Element-Binding Protein metabolism, Drosophila Proteins metabolism, MAP Kinase Kinase 4 metabolism, Pseudomonas Infections metabolism, Wounds and Injuries metabolism
- Abstract
In mammals, both sterile wounding and infection induce inflammation and activate the innate immune system, and the combination of both challenges may lead to severe health defects, revealing the importance of the balance between the intensity and resolution of the inflammatory response for the organism's fitness. Underlying mechanisms remain however elusive. Using Drosophila, we show that, upon infection with the entomopathogenic bacterium Pseudomonas entomophila (Pe), a sterile wounding induces a reduced resistance and increased host mortality. To identify the molecular mechanisms underlying the susceptibility of wounded flies to bacterial infection, we analyzed the very first steps of the process by comparing the transcriptome landscape of infected (simple hit flies, SH), wounded and infected (double hit flies, DH) and wounded (control) flies. We observed that overexpressed genes in DH flies compared to SH ones are significantly enriched in genes related to stress, including members of the JNK pathway. We demonstrated that the JNK pathway plays a central role in the DH phenotype by manipulating the Jra/dJun activity. Moreover, the CrebA/Creb3-like transcription factor (TF) and its targets were up-regulated in SH flies and we show that CrebA is required for mounting an appropriate immune response. Drosophila thus appears as a relevant model to investigate interactions between trauma and infection and allows to unravel key pathways involved.
- Published
- 2017
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16. Platelet function is modified by common sequence variation in megakaryocyte super enhancers.
- Author
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Petersen R, Lambourne JJ, Javierre BM, Grassi L, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP, Jiang T, Farrow S, Cairns J, Al-Subaie AM, Ashford S, Attwood A, Batista J, Bouman H, Burden F, Choudry FA, Clarke L, Flicek P, Garner SF, Haimel M, Kempster C, Ladopoulos V, Lenaerts AS, Materek PM, McKinney H, Meacham S, Mead D, Nagy M, Penkett CJ, Rendon A, Seyres D, Sun B, Tuna S, van der Weide ME, Wingett SW, Martens JH, Stegle O, Richardson S, Vallier L, Roberts DJ, Freson K, Wernisch L, Stunnenberg HG, Danesh J, Fraser P, Soranzo N, Butterworth AS, Heemskerk JW, Turro E, Spivakov M, Ouwehand WH, Astle WJ, Downes K, Kostadima M, and Frontini M
- Subjects
- Chromatin, Humans, Promoter Regions, Genetic, Blood Platelets physiology, Enhancer Elements, Genetic, Erythroblasts chemistry, Genetic Variation, Megakaryocytes chemistry
- Abstract
Linking non-coding genetic variants associated with the risk of diseases or disease-relevant traits to target genes is a crucial step to realize GWAS potential in the introduction of precision medicine. Here we set out to determine the mechanisms underpinning variant association with platelet quantitative traits using cell type-matched epigenomic data and promoter long-range interactions. We identify potential regulatory functions for 423 of 565 (75%) non-coding variants associated with platelet traits and we demonstrate, through ex vivo and proof of principle genome editing validation, that variants in super enhancers play an important role in controlling archetypical platelet functions.
- Published
- 2017
- Full Text
- View/download PDF
17. Identification and in silico modeling of enhancers reveals new features of the cardiac differentiation network.
- Author
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Seyres D, Ghavi-Helm Y, Junion G, Taghli-Lamallem O, Guichard C, Röder L, Girardot C, Furlong EE, and Perrin L
- Subjects
- Animals, Animals, Genetically Modified, Cell Differentiation genetics, Chromatin, Drosophila genetics, Gene Regulatory Networks genetics, Histones metabolism, Organogenesis physiology, Transcription Factors genetics, Drosophila embryology, Enhancer Elements, Genetic genetics, Gene Expression Regulation, Developmental genetics, Heart embryology, Myocytes, Cardiac cytology, Organogenesis genetics, Promoter Regions, Genetic genetics
- Abstract
Developmental patterning and tissue formation are regulated through complex gene regulatory networks (GRNs) driven through the action of transcription factors (TFs) converging on enhancer elements. Here, as a point of entry to dissect the poorly defined GRN underlying cardiomyocyte differentiation, we apply an integrated approach to identify active enhancers and TFs involved in Drosophila heart development. The Drosophila heart consists of 104 cardiomyocytes, representing less than 0.5% of all cells in the embryo. By modifying BiTS-ChIP for rare cells, we examined H3K4me3 and H3K27ac chromatin landscapes to identify active promoters and enhancers specifically in cardiomyocytes. These in vivo data were complemented by a machine learning approach and extensive in vivo validation in transgenic embryos, which identified many new heart enhancers and their associated TF motifs. Our results implicate many new TFs in late stages of heart development, including Bagpipe, an Nkx3.2 ortholog, which we show is essential for differentiated heart function., (© 2016. Published by The Company of Biologists Ltd.)
- Published
- 2016
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18. LedPred: an R/bioconductor package to predict regulatory sequences using support vector machines.
- Author
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Seyres D, Darbo E, Perrin L, Herrmann C, and González A
- Subjects
- Animals, Computer Graphics, Drosophila, Gene Expression Regulation, Metabolic Networks and Pathways, Mice, Systems Integration, Molecular Sequence Annotation, Software, Support Vector Machine
- Abstract
Unlabelled: Supervised classification based on support vector machines (SVMs) has successfully been used for the prediction of cis-regulatory modules (CRMs). However, no integrated tool using such heterogeneous data as position-specific scoring matrices, ChIP-seq data or conservation scores is currently available. Here, we present LedPred, a flexible SVM workflow that predicts new regulatory sequences based on the annotation of known CRMs, which are associated to a large variety of feature types. LedPred is provided as an R/Bioconductor package connected to an online server to avoid installation of non-R software. Due to the heterogeneous CRM feature integration, LedPred excels at the prediction of regulatory sequences in Drosophila and mouse datasets compared with similar SVM-based software., Availability and Implementation: LedPred is available on GitHub: https://github.com/aitgon/LedPred and Bioconductor: http://bioconductor.org/packages/release/bioc/html/LedPred.html under the MIT license., Contact: aitor.gonzalez@univ-amu.fr, Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2016
- Full Text
- View/download PDF
19. Identification of cis-regulatory modules encoding temporal dynamics during development.
- Author
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Potier D, Seyres D, Guichard C, Iche-Torres M, Aerts S, Herrmann C, and Perrin L
- Subjects
- Animals, Base Sequence, Computer Simulation, Drosophila Proteins biosynthesis, Drosophila Proteins genetics, Drosophila melanogaster growth & development, Drosophila melanogaster metabolism, Enhancer Elements, Genetic, Genes, Reporter, Green Fluorescent Proteins biosynthesis, Green Fluorescent Proteins genetics, Heart physiology, Larva genetics, Larva growth & development, Larva metabolism, Limit of Detection, Metamorphosis, Biological, Molecular Sequence Data, ROC Curve, Regulatory Sequences, Nucleic Acid, Transcription Factors physiology, Transcriptional Activation, Transcriptome, beta-Galactosidase biosynthesis, beta-Galactosidase genetics, Drosophila melanogaster genetics, Gene Expression Regulation, Developmental
- Abstract
Background: Developmental transcriptional regulatory networks are circuits of transcription factors (TFs) and cis-acting DNA elements (Cis Regulatory Modules, CRMs) that dynamically control expression of downstream genes. Comprehensive knowledge of these networks is an essential step towards our understanding of developmental processes. However, this knowledge is mostly based on genome-wide mapping of transcription factor binding sites, and therefore requires prior knowledge regarding the TFs involved in the network., Results: Focusing on how temporal control of gene expression is integrated within a developmental network, we applied an in silico approach to discover regulatory motifs and CRMs of co-expressed genes, with no prior knowledge about the involved TFs. Our aim was to identify regulatory motifs and potential trans-acting factors which regulate the temporal expression of co-expressed gene sets during a particular process of organogenesis, namely adult heart formation in Drosophila. Starting from whole genome tissue specific expression dynamics, we used an in silico method, cisTargetX, to predict TF binding motifs and CRMs. Potential Nuclear Receptor (NR) binding motifs were predicted to control the temporal expression profile of a gene set with increased expression levels during mid metamorphosis. The predicted CRMs and NR motifs were validated in vivo by reporter gene essays. In addition, we provide evidence that three NRs modulate CRM activity and behave as temporal regulators of target enhancers., Conclusions: Our approach was successful in identifying CRMs and potential TFs acting on the temporal regulation of target genes. In addition, our results suggest a modular architecture of the regulatory machinery, in which the temporal and spatial regulation can be uncoupled and encoded by distinct CRMs.
- Published
- 2014
- Full Text
- View/download PDF
20. Ndae1 expression and regulation in Drosophila embryos.
- Author
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Tevy MF, Seyres D, Traina C, Perrin L, and Capovilla M
- Subjects
- Animals, Antiporters metabolism, Drosophila Proteins metabolism, Embryonic Development genetics, Gene Expression, Gene Order, Genes, Reporter, Genetic Loci, Introns, Mutation, Regulatory Sequences, Nucleic Acid, Antiporters genetics, Drosophila embryology, Drosophila genetics, Drosophila Proteins genetics, Embryo, Nonmammalian, Gene Expression Regulation, Developmental
- Abstract
The construction and prediction of cell fate maps at the whole embryo level require the establishment of an accurate atlas of gene expression patterns throughout development and the identification of the corresponding cis-regulatory sequences. However, while the expression and regulation of genes encoding upstream developmental regulators such as transcription factors or signaling pathway components have been analyzed in detail, up to date the number of cis-regulatory sequences identified for downstream effector genes, like ion channels, pumps and exchangers, is very low. The control and regulation of ion homeostasis in each cell, including at blastoderm stages, are essential for normal embryonic development. In this study, we analyzed in detail the embryonic expression pattern and cis-regulatory modules of the Drosophila Na+-driven anion exchanger 1 (Ndae1) gene, involved in the regulation of pH homeostasis. We show that Ndae1 is expressed in a tight and complex spatial-temporal pattern. In particular, we report that this downstream effector gene is under the control of the canonical dorsal-ventral patterning cascade through dorsal, Toll, twist and snail at early embryogenesis. Moreover, we identify several cis-regulatory modules, some of which control discrete and non-overlapping aspects of endogenous gene expression throughout development.
- Published
- 2014
- Full Text
- View/download PDF
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