In vivo conditional deletion of HDAC7 reveals its requirement to establish proper B lymphocyte identity and development

Class IIa histone deacetylase (HDAC) subfamily members are tissue-specific gene repressors with crucial roles in development and differentiation processes. A prominent example is HDAC7, a class IIa HDAC that shows a lymphoid-specific expression pattern within the hematopoietic system. In this study, we explored its potential role in B cell development by generating a conditional knockout mouse model. Our study demonstrates for the first time that HDAC7 deletion dramatically blocks early B cell development and gives rise to a severe lymphopenia in peripheral organs, while also leading to pro-B cell lineage promiscuity. We find that HDAC7 represses myeloid and T lymphocyte genes in B cell progenitors through interaction with myocyte enhancer factor 2C (MEFC2). In B cell progenitors, HDAC7 is recruited to promoters and enhancers of target genes, and its absence leads to increased enrichment of histone active marks. Our results prove that HDAC7 is a bona fide transcriptional repressor essential for B cell development

Defective minor spliceosome mRNA processing results in isolated familial growth hormone deficiency

The molecular basis of a significant number of cases of isolated growth hormone deficiency remains unknown. We describe three sisters affected with severe isolated growth hormone deficiency and pituitary hypoplasia caused by biallelic mutations in the RNPC3 gene, which codes for a minor spliceosome protein required for U11/U12 small nuclear ribonucleoprotein (snRNP) formation and splicing of U12-type introns. We found anomalies in U11/U12 di-snRNP formation and in splicing of multiple U12-type introns in patient cells. Defective transcripts include preprohormone convertases SPCS2 and SPCS3 and actin-related ARPC5L genes, which are candidates for the somatotroph-restricted dysfunction. The reported novel mechanism for familial growth hormone deficiency demonstrates that general mRNA processing defects of the minor spliceosome can lead to very narrow tissue-specific consequences.Peer reviewe

Detection of chromothripsis-like patterns with a custom array platform for chronic lymphocytic leukemia

This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License.-- et al.Chronic lymphocytic leukemia (CLL) is a common disease with highly variable clinical course. Several recurrent chromosomal alterations are associated with prognosis and may guide risk-adapted therapy. We have developed a targeted genome-wide array to provide a robust tool for ascertaining abnormalities in CLL and to overcome limitations of the 4-marker fluorescence in situ hybridization (FISH). DNA from 180 CLL patients were hybridized to the qChip®Hemo array with a high density of probes covering commonly altered loci in CLL (11q22-q23, 13q14, and 17p13), nine focal regions (2p15-p16.1, 2p24.3, 2q13, 2q36.3-q37.1, 3p21.31, 8q24.21, 9p21.3, 10q24.32, and 18q21.32-q21.33) and two larger regions (6q14.1-q22.31 and 7q31.33-q33). Overall, 86% of the cases presented copy number alterations (CNA) by array. There was a high concordance of array findings with FISH (84% sensitivity, 100% specificity); all discrepancies corresponded to subclonal alterations detected only by FISH. A chromothripsis-like pattern was detected in eight cases. Three showed concomitant shattered 5p with gain of TERT along with isochromosome 17q. Presence of 11q loss was associated with shorter time to first treatment (P=0.003), whereas 17p loss, increased genomic complexity, and chromothripsis were associated with shorter overall survival (P<0.001, P=0.001, and P=0.02, respectively). In conclusion, we have validated a targeted array for the diagnosis of CLL that accurately detects, in a single experiment, all relevant CNAs, genomic complexity, chromothripsis, copy number neutral loss of heterozygosity, and CNAs not covered by the FISH panel. This test may be used as a practical tool to stratify CLL patients for routine diagnostics or clinical trials.Supported by: Fondo de Investigaciones Sanitarias, Instituto de Salud Carlos III (ISCIII), Grant numbers: PI11/01177, PI14/00571; Worldwide Cancer Research; Grant number: 12-0142; Marato de TV3; Grant number: TV3-Cancer/2013410; Generalitat de Catalunya Suport Grups de Recerca; Grant number: 2013-SGR-378; Red Tematica de Investigacion Cooperativa en Cancer (RTICC), Grant numbers: RD12/0036/0036, RD12/0036/0023, RD12/0036/0004, RD12/0036/0069; Subprograma Juan de la Cierva, Grant number: JCI-2011-10232; Miguel Servet Contract, Grant number: CP13/00159; the Spanish Ministry of Science and Innovation (MICINN) through the ISCIII —International Cancer Genome Consortium for Chronic Lymphocytic Leukemia (ICGC-CLL Genome Project); Institucio Catalana de Recerca i Estudis Avançats” (ICREA) of the Generalitat de Catalunya; European Regional Development Fund “Una manera de fer Europa”; Alexander von Humboldt Post-doctoral Fellowship.Peer Reviewe

Detectable clonal mosaicism in blood as biomarker of cancer risk in Fanconi anemia

Altres ajuts: Juan de la Cierva postdoctoral fellowship (JCI-2011-10660); Marató de TV3 (project 464/C/2012)Detectable clonal mosaicism for large chromosomal events has been associated with aging and an increased risk of hematological and some solid cancers. We hypothesized that genetic cancer predisposition disorders, such as Fanconi anemia (FA), could manifest a high rate of chromosomal mosaic events (CMEs) in peripheral blood, which could be used as early biomarkers of cancer risk. We studied the prevalence of CMEs by single-nucleotide polymorphism (SNP) array in 130 FA patients' blood DNA and their impact on cancer risk. We detected 51 CMEs (4.4-159 Mb in size) in 16 out of 130 patients (12.3%), of which 9 had multiple CMEs. The most frequent events were gains at 3q (n = 6) and 1q (n = 5), both previously associated with leukemia, as well as rearrangements with breakpoint clustering within the major histocompatibility complex locus (P = 7.3 × 10-9). Compared with 15?743 age-matched population controls, FA patients had a 126 to 140 times higher risk of detectable CMEs in blood (P < 2.2 × 10-16). Prevalent and incident hematologic and solid cancers were more common in CME carriers (odds ratio [OR] = 11.6, 95% confidence interval [CI] = 3.4-39.3, P = 2.8 × 10-5), leading to poorer prognosis. The age-adjusted hazard risk (HR) of having cancer was almost 5 times higher in FA individuals with CMEs than in those without CMEs. Regarding survival, the HR of dying was 4 times higher in FA individuals having CMEs (HR = 4.0, 95% CI = 2.0-7.9, P = 5.7 × 10-5). Therefore, our data suggest that molecular karyotyping with SNP arrays in easy-to-obtain blood samples could be used for better monitoring of bone marrow clonal events, cancer risk, and overall survival of FA patients

Estructura del genoma

El genoma és una estructura altament dinàmica amb una certa tendència a la inestabilitat, i està, per tant, subjecte a l'escrutini de la selecció natural. En el camí d'entendre el genoma hem pogut observar el paper clau que tenen les repeticions (de tota mena) per comprendre l'evolució estructural del genoma humà i com es relaciona l'estructura i la funció. Així, recentment, hem pogut apreciar que, a part de les variacions clàssiques i els SNP (polimorfismes d'un sol nucleòtid), els mamífers (com a mínim els ratolins i els humans) tenim una estructura dels nostres genomes altament variable. L'estudi de les regions variants en nombre de còpia (structural variants o copy number polymorphism) ens ha permès observar que els canvis en l'estructura tenen repercussió en l'expressió dels gens, que es tradueixen tant en variabilitat fenotípica entre individus com, en casos més extrems, en malalties. En aquest capítol donarem una visió sobre l'estructura i el dinamisme del genoma, centrantnos en aspectes evolutius del polimorfisme humà i la malaltia.Every mammalian genome is an unstable and highly dynamic structure and therefore subjected to the strict evaluation of natural selection. In the last decades, we have changed our vocabulary and we have been using genomics instead of genetics, mainly because of the revolution on our research techniques. In the way of the understanding of the genomes, we realized how important repeats are and their role in the evolution of the structure of the human genome and how this structure and different functions are related. We have seen for instance that besides of the variation caused for SNPs (Single Nucleotide Polymorphism), the mammals (and specifically humans) are highly structural variant. The study of SVs (Structural Variant regions) and CNPs (Copy Number Polymorphisms) has allowed us to see that changes in structure have important consequences, from genomic diseases to simply affecting genes and its expression and hence, being responsible of the huge phenotypical variability observed among individuals. In this chapter, we will give our view on the structure and dynamism of the genome, from an evolutionary point of view, covering human polymorphism and diseases

Clinical implication of FMR1 intermediate alleles in a Spanish population

FMR1 premutation carriers (55-200 CGGs) are at risk of developing Fragile X-associated primary ovarian insufficiency as well as Fragile X-associated tremor/ataxia syndrome. FMR1 premutation alleles are also associated with a variety of disorders, including psychiatric, developmental, and neurological problems. However, there is a major concern regarding clinical implications of smaller CGG expansions known as intermediate alleles (IA) or gray zone alleles (45-54 CGG). Although several studies have hypothesized that IA may be involved in the etiology of FMR1 premutation associated phenotypes, this association still remains unclear. The aim of this study was to provide new data on the clinical implications of IA. We reviewed a total of 17 011 individuals: 1142 with primary ovarian insufficiency, 478 with movement disorders, 14 006 with neurodevelopmental disorders and 1385 controls. Similar IA frequencies were detected in all the cases and controls (cases 1.20% vs controls 1.39%, P =.427). When comparing the allelic frequencies of IA = 50CGGs, a greater, albeit not statistically significant, number of alleles were detected in all the cohorts of patients. Therefore, IA below 50 CGGs should not be considered as risk factors for FMR1 premutation-associated phenotypes, at least in our population. However, the clinical implication of IA = 50CGGs remains to be further elucidated

GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing

The combined analysis of haplotype panels with phenotype clinical cohorts is a common approach to explore the genetic architecture of human diseases. However, genetic studies are mainly based on single nucleotide variants (SNVs) and small insertions and deletions (indels). Here, we contribute to fill this gap by generating a dense haplotype map focused on the identification, characterization, and phasing of structural variants (SVs). By integrating multiple variant identification methods and Logistic Regression Models (LRMs), we present a catalogue of 35 431 441 variants, including 89 178 SVs (≥50 bp), 30 325 064 SNVs and 5 017 199 indels, across 785 Illumina high coverage (30x) whole-genomes from the Iberian GCAT Cohort, containing a median of 3.52M SNVs, 606 336 indels and 6393 SVs per individual. The haplotype panel is able to impute up to 14 360 728 SNVs/indels and 23 179 SVs, showing a 2.7-fold increase for SVs compared with available genetic variation panels. The value of this panel for SVs analysis is shown through an imputed rare Alu element located in a new locus associated with Mononeuritis of lower limb, a rare neuromuscular disease. This study represents the first deep characterization of genetic variation within the Iberian population and the first operational haplotype panel to systematically include the SVs into genome-wide genetic studies