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Miguel-Escalada I, Bonàs.Guarch S, Cebola I, Mendieta-Esteban,, Rolando DMY, Javierre B, Goutham A, Irene I, Morgan CC, García-Hurtado J, Beucher A, Morán I, Pasquali L, Ramos M, Appel EVR, Linneberg A, Gjesing PD, Witte R, Pederson O, Grarup N, Ravassard P, Torrents D, Kerr-Conte J, Pattou F, Fedko IO, Prokopenko I, Hansen T, Martí-Renom, Fraser P, Ferrer J

Human pancreatic islet 3D chromatin architecture provides insights into the genetics of type 2 diabetes

Nature Genetics (in press at 7 May 2019, .
Genetic studies promise to provide insight into the molecular mechanisms underlying type 2 diabetes (T2D). Variants associated with T2D are often located in tissue-specific enhancer regions (enhancer clusters, stretch enhancers or super-enhancers). So far, such domains have been defined through clustering of enhancers in linear genome maps rather than in 3D-space. Furthermore, their target genes are generally unknown. We have now created promoter capture Hi-C maps in human pancreatic islets. This linked diabetes-associated enhancers with their target genes, often located hundreds of kilobases away. It further revealed sets of islet enhancers, super-enhancers and active promoters that form 3D higher-order hubs, some of which show coordinated glucose-dependent activity. Hub genetic variants impact the heritability of insulin secretion, and help identify individuals in whom genetic variation of islet function is important for T2D. Human islet 3D chromatin architecture thus provides a framework for interpretation of T2D GWAS signals.
Watt S, Vasquez L, Walter K, Mann AL, Kundu K, Chen Lu, Yan Y, Ecker S, Burden F, Farrow S, Farr B, Iotchkova V, Elding H, Mead D, Tardaguila M, Ponstingl H, Fraser P, Richardson D, Datta A, Flicek P, Clarke L, Downes K, Pastinen T, Fraser P, Frontini M, Javierre BM, Spivakov M, Soranzo N

Variation in PU.1 binding and chromatin looping at neutrophil enhancers influences autoimmune disease susceptibility

bioRxiv 29 Abr 2019, . Epub 29 Abr 2019
Neutrophils play fundamental roles in innate inflammatory response, shape adaptive immunity1, and have been identified as a potentially causal cell type underpinning genetic associations with immune system traits and diseases2,3 The majority of these variants are non-coding and the underlying mechanisms are not fully understood. Here, we profiled the binding of one of the principal myeloid transcriptional regulators, PU.1, in primary neutrophils across nearly a hundred volunteers, and elucidate the coordinated genetic effects of PU.1 binding variation, local chromatin state, promoter-enhancer interactions and gene expression. We show that PU.1 binding and the associated chain of molecular changes underlie genetically-driven differences in cell count and autoimmune disease susceptibility. Our results advance interpretation for genetic loci associated with neutrophil biology and immune disease.
Ribera JM, García O, Moreno MJ, Barba P, García-Cadenas I, Mercadal S, Montesinos P, Barrios M, González-Campos J, Martínez-Carballeira D, Gil C, Ribera J, Vives S, Novo A, Cervera M, Serrano J, Lavilla E, Abella E, Tormo M, Amigo ML, Artola MT, Genescà E, Bravo P, García-Belmonte D, García-Guiñón A, Hernández-Rivas JM, Feliu E

Incidence and outcome after first molecular versus overt recurrence in patients with Philadelphia chromosome-positive acute lymphoblastic leukemia included in the ALL Ph08 trial from the Spanish PETHEMA Group.

Cancer 23 Abr 2019, . Epub 23 Abr 2019
Disease recurrence occurs in 20% to 40% of adults with Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ ALL) who are treated with chemotherapy and tyrosine kinase inhibitors (TKIs). In the current study, the authors report the incidence, treatment, and outcome after first disease recurrence in young and older adults treated in the ALL Ph08 trial (ClinicalTrials.gov identifier NCT01491763).
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Ganster C, Müller-Thomas C, Haferlach C, Strupp C, Ogata K, Germing U, Hildebrandt B, Mallo M, Lübbert M, Müller C, Solé F, Götze KS, Vandenberghe P, Göhring G, Steinmetz T, Kröger N, Platzbecker U, Söling U, Raynaud S, Shirneshan K, Schanz J, Haase D

Comprehensive analysis of isolated der(1;7)(q10;p10) in a large international homogenous cohort of patients with myelodysplastic syndromes.

Genes Chromosomes Cancer 17 Abr 2019, . Epub 17 Abr 2019
The karyotype is a strong independent prognostic factor in myelodysplastic syndromes (MDS). Since the implementation of the new comprehensive cytogenetic scoring system for MDS, chromosome 7 anomalies are no longer generally assigned to poor risk features but are thoroughly separated. However, der(1;7)(q10;p10), hereinafter der(1;7), is merged into the group labeled "any other single" and belongs to the intermediate risk group, just by definition due to lack of adequate clinical data. The aim of our international collaborative was to clarify the "real" prognostic impact of der(1;7) on a homogenous and well-documented data base. We performed detailed analysis of 63 MDS patients with isolated der(1;7) constituting the largest cohort hitherto reported. Furthermore, clinical data are compared with those of patients with isolated del(7q) and isolated monosomy 7. Median overall survival (OS) of patients with der(1;7) is 26 months (hazard ratio (HR) 0.91 for del(7q) vs der(1;7) and 2.53 for monosomy 7 vs der(1;7)). The der(1;7) is associated with profound thrombocytopenia most probably causing the reduced OS which is in striking contrast to the low risk for AML transformation (HR 3.89 for del(7q) vs der(1;7) and 5.88 for monosomy 7 vs der(1;7)). Molecular karyotyping indicates that der(1;7) is generated in a single step during mitosis and that a chromosomal imbalance rather than a single disrupted gene accounts for malignancy. Thus, the current cytogenetic scoring system assigning isolated der(1;7) to the intermediate risk group is now confirmed by a sufficient data set.
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Ribera J, Granada I, Morgades M, Vives S, Genescà E, González C, Nomdedeu J, Escoda L, Montesinos P, Mercadal S, Coll R, González-Campos J, Abella E, Barba P, Bermúdez A, Gil C, Tormo M, Pedreño M, Martínez-Carballeira D, Hernández-Rivas JM, Orfao A, Martínez-López J, Esteve J, Bravo P, Garcia-Guiñon A, Debén G, Moraleda JM, Queizán JA, Ortín X, Moreno MJ, Feliu E, Solé F, Ribera JM

The poor prognosis of low hypodiploidy in adults with B-cell precursor acute lymphoblastic leukaemia is restricted to older adults and elderly patients.

Br. J. Haematol. 27 Mar 2019, . Epub 27 Mar 2019
The prognostic significance of low-hypodiploidy has not been extensively evaluated in minimal residual disease (MRD)-oriented protocols for adult acute lymphoblastic leukaemia (ALL). We analysed the outcome of hypodiploid adult ALL patients treated within Programa Español de Tratamientos en Hematología (PETHEMA) protocols. The 5-year cumulative incidence of relapse (CIR) of low-hypodiploid B-cell precursor (BCP)-ALL was significantly higher than that of high-hypodiploids (52% vs. 12%, P = 0.013). Low-hypodiploid BCP-ALL patients aged ≤35 years showed superior survival (71% vs. 21%, P = 0.026) and lower 5-year CIR (17% vs. 66%, P = 0.090) than low-hypodiploids aged >35 years. Older adults and elderly low-hypodiploid BCP-ALL patients show dismal prognosis although achieving an end-induction good MRD response.
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