Genetic analysis of over one million people identifies 535 novel loci for blood pressure

High blood pressure is the foremost heritable global risk factor for cardiovascular disease. We report the largest genetic association study of blood pressure traits to date (systolic, diastolic, pulse pressure) in over one million people of European ancestry. We identify 535 novel blood pressure loci that not only offer new biological insights into blood pressure regulation but also reveal shared loci influencing lifestyle exposures. Our findings offer the potential for a precision medicine strategy for future cardiovascular disease prevention

Genetic correlation and causal relationships between cardio-metabolic traits and Lung function Impairment

Background Associations of low lung function with features of poor cardio-metabolic health have been reported. It is, however, unclear whether these co-morbidities reflect causal associations, shared genetic heritability or are confounded by environmental factors. Methods We performed three analyses: 1) cardio-metabolic health to lung function association tests in NFBC1966, 2) cross trait LD score regression to compare genetic backgrounds and 3) Mendelian Randomization (MR) analysis to assess the causal effect of cardio-metabolic traits and disease on lung function, and vice versa (bidirectional MR). Genetic associations were obtained from UK Biobank data or published large-scale genome-wide association studies (N > 82,000). Results We observed negative genetic correlation between lung function and cardio-metabolic traits and diseases. In Mendelian Randomisation analysis (MR) we found associations between Type 2 Diabetes instruments and FVC as well as FEV1/FVC. BMI instruments were associated to all lung function traits and CRP instruments to FVC. These genetic association provide evidence for a causal effect of cardio-metabolic traits on lung function. Multivariable MR suggested independence of these causal effects from other tested cardio-metabolic traits and diseases. Analysis of lung function specific SNPs revealed a potential causal effect of FEV1/FVC on blood pressure. Conclusions The present study overcomes many limitations of observational studies by using Mendelian Randomisation. We provide evidence for an independent causal effect of T2D, CRP and BMI on lung function with some of the T2D effect on lung function being mediated by CRP. Furthermore, this analysis suggests a potential causal effect of FEV1/FVC on blood pressure. Our detailed analysis of the interplay between cardio-metabolic traits and impaired lung function provides the opportunity to improve the quality of existing intervention strategies

RNA-Seq De Novo Assembly of Clonal Immunoglobulin Rearrangements Identifies Interesting Biology and Uncovers Prognostic Features in Multiple Myeloma

Introduction Although monoclonal immunoglobulin (Ig) production by myeloma cells is one of the central features of the disease, genotypic identification of the clonal Ig sequence remains understudied in multiple myeloma (MM). Here, using extensive RNA-seq data, we study molecular features of clonal Ig rearrangements, as well as their association with other MM markers and patient outcome. Methods We performed deep RNA-seq on purified CD138+ MM cells from 429 newly-diagnosed uniformly-treated patients with long clinical follow-up. For each sample, we performed de novo assembly using sequences that appeared in the library with a frequency of at least one in a million. Germline V and J genes were then BLASTed against the assembled contigs to determine the clonal germline genes and pinpoint mutations. Using the sequences reconstructed from the Ig contigs and the BLAST output, we ran IgBLAST to fully characterize the predominant Ig V(D)J sequence. Results We tested the accuracy of our approach by looking at 24 technical duplicates and one triplicate. In all cases, the predicted gene and gene allele were consistent across replicates. Next, we evaluated our large patient cohort, identifying IGHV3 as the most common clonal VH gene subgroup (53.3%), followed by IGHV4 (17.8%) and IGHV1 (15.6%). Importantly, we observed a significant association between poorer prognosis and IGHV3, both for progression-free survival (PFS) (p=0.0019) and overall survival (OS) (p=0.012). IGHV3-30 (11%, the most commonly rearranged VH gene) and IGHV3-9 (4.8%) were the drivers behind this poor prognosis (IGHV3-30: PFS p=0.021; OS p=0.013) (IGHV3-9: PFS p=0.002). IGHV3-30 was even more preferentially rearranged than in normal B-cell VH repertoires from previous studies (8.5%, 6.3%) and ours (2%). Remarkably, these results sharply contrast with what has been observed in CLL. In this malignancy, IGHV3-30 use has been seen to be underrepresented and usually characterizes an indolent clinical course, while IGHV3-21 and possibly IGHV3-23 carry poor prognosis. We predicted light chain usage through the presence of clonal VL sequences. The most frequent VL genes were from the \u3ba locus (69.4% total): IGKV1-33 (12.4%), IGKV1-5 (11.3%), IGKV3-20 (9.9%) and IGKV1-39 (8.0%). Del(22q) was observed more frequently in patients with IG\u3bb (OR=10.0, p=6e-15) and, within this group, del(22q) was more frequent if V\u3bb belonged to the more centromeric V-clusters C or B, in contrast to cluster A (OR=8.4, p=5e-4). Remarkably, patients with V\u3bb gene from cluster A presented worse OS (vs. Vk: p=0.0079; vs. V\u3bb B,C: p=0.067). The proportion of mutated bases was higher in the heavy chain than in the light chain (mean 7.0% vs. 4.8%, max 14.6% vs. 14.3%), and it was associated with OS (heavy p=0.0020, light p=0.036, both=0.0056), but not PFS. Interestingly, mutated Ig in CLL results in a more benign clinical course. We further found that 24.9% and 22.7% of the mutations lay within WRCY or RGYW AID motifs in the light and heavy chains respectively (enrichment p<1e-16), while AID mutations in a TW or WA context accounted for 22.9% and 25.7% (p=0.14, p=0.64). Higher ratios of mutations in WRCY vs. RGYW motifs within the light chain were highly predictive of poor prognosis (PFS p=0.0019, OS p=6.3e-4). Strikingly, IG\u3bb usage was linked to higher ratios (p=3e-6), an association not explained by germline sequence variability (p=0.24). The usage of IGHV3 genes and the AID WRCY/RGYW motif ratio were independent markers of each other (p=1) and of other markers of poor prognosis in MM, such as presence of either t(4;14) or del(17p) (IGHV3 p=0.10; motif ratio p=0.49). In conclusion, de novo Ig heavy and light chain assembly using RNA-seq identifies interesting biology, may provide MM markers and highlights a novel application of high-throughput genomics

Redefining Mutational Profiling Using RNA-Seq: Insight into the Functional Mutational Landscape of Multiple Myeloma

Whole genome and exome sequencing (WGS, WES) have enabled the identification of mutational signatures in Multiple Myeloma (MM) and other cancer types. In studies that assess the impact of coding mutations on protein structure and function, only reads mapping to the exome are pertinent. Thus, WES is typically preferred over WGS, as it provides deeper coverage given the same amount of total reads. However, exome enrichment - a necessary step in WES, limits the ability to call mutations, as coverage is restricted to the capture regions and affected by their GC content. Furthermore, without transcriptional information, it is not possible to determine which coding mutations found by WGS or WES are expressed and, therefore, more likely to be relevant. As an alternative, RNA-seq data directly targets the transcriptome, providing deep coverage, not requiring an enrichment step and intrinsically omitting non-expressed mutations. Moreover, when RNA-seq data is already available for evaluation of gene expression profiles, one can further leverage the data to explore expressed mutational profiles. However, limitations in pipelines to analyze RNA-seq data have restricted their applicability so far. Using paired WES and RNA-seq data from MM patient samples, we have observed that the majority of recurrent mutations in MM occur within genes with very low or no detectable expression (only 27% of mutated genes express). Here, we have further analyzed a large RNA-seq sample set to describe a comprehensive transcriptional mutational landscape in MM and identify potential mutational driver genes. Specifically, we performed RNA-seq on CD138+ MM cells from 292 newly-diagnosed patients and 16 normal bone marrow plasma cell (NBM) samples. The unstranded 50bp paired-end reads were mapped to the human genome using MapSplice followed by a workflow for variant analysis based on GATK. Output was filtered for germline variants and technical artifacts, then evaluated computationally for functional impact, and finally further filtered at the gene level. Using this workflow we were able to identify most reported recurrently mutated genes in MM, including but not limited to TP53 (14%), NRAS (14%), KRAS (11%), ACTG1 (4%), CCND1 (4%), TRAF3 (3%), FAM46C (3%), CYLD (3%) and DIS3 (2%). Importantly, we were also able to identify novel putative mutational driver genes of lower frequency, including several genes involved in the NF-\u3baB pathway (BCR, TAOK2, NFKBIA, PIM1) and genes coding for proteins forming the mTORC2 complex (SIN1, RICTOR, MTOR). We observe that the average mutational frequency, which is a convolution of clonality and relative allelic expression, is slightly below 0.5. Yet, we find diverse mutational frequencies across samples for each given gene. For instance, FAM46C shows a pattern representative of highly subclonal mutations, whereas CCND1 presents mostly bi-allelic and clonal mutations, and others such as TRAF3 show a wide spectrum of mutational frequencies. Further developments will be needed to deconvolve these frequencies. We also applied the workflow to 10 of the samples for which we reported mutations at the DNA level, and observe CCND1, TP53 and KRAS to be recurrently mutated using either WES or RNA-seq. Nevertheless, some mutations are not shared, including 3 WES-exclusive BRAF mutations and one seen in CCND1 through RNA-seq only. In conclusion, we report the first computational analysis to identify mutational driver genes using RNA-seq data, providing additional insight into the mutational landscape of MM. Our findings demonstrate that RNA-seq of unpaired tumor samples can suffice to characterize the most salient characteristics of cancer mutational landscapes

Genetic correlation and causal relationships between cardio-metabolic traits and lung function impairment

Abstract Background: Associations of low lung function with features of poor cardio-metabolic health have been reported. It is, however, unclear whether these co-morbidities reflect causal associations, shared genetic heritability or are confounded by environmental factors. Methods: We performed three analyses: (1) cardio-metabolic health to lung function association tests in Northern Finland Birth cohort 1966, (2) cross-trait linkage disequilibrium score regression (LDSC) to compare genetic backgrounds and (3) Mendelian randomisation (MR) analysis to assess the causal effect of cardio-metabolic traits and disease on lung function, and vice versa (bidirectional MR). Genetic associations were obtained from the UK Biobank data or published large-scale genome-wide association studies (N &gt; 82,000). Results: We observed a negative genetic correlation between lung function and cardio-metabolic traits and diseases. In Mendelian Randomisation analysis (MR), we found associations between type 2 diabetes (T2D) instruments and forced vital capacity (FVC) as well as FEV1/FVC. Body mass index (BMI) instruments were associated to all lung function traits and C-reactive protein (CRP) instruments to FVC. These genetic associations provide evidence for a causal effect of cardio-metabolic traits on lung function. Multivariable MR suggested independence of these causal effects from other tested cardio-metabolic traits and diseases. Analysis of lung function specific SNPs revealed a potential causal effect of FEV1/FVC on blood pressure. Conclusions: The present study overcomes many limitations of observational studies by using Mendelian Randomisation. We provide evidence for an independent causal effect of T2D, CRP and BMI on lung function with some of the T2D effect on lung function being attributed to inflammatory mechanisms. Furthermore, this analysis suggests a potential causal effect of FEV1/FVC on blood pressure. Our detailed analysis of the interplay between cardio-metabolic traits and impaired lung function provides the opportunity to improve the quality of existing intervention strategies

Loss of Tribbles pseudokinase-3 promotes Akt-driven tumorigenesis via FOXO inactivation

This work was supported by grants from Spanish Ministry of Economy and Competitiveness (MINECO) and Fondo Europeo de Desarrollo Regional (FEDER) (PS09/01401; PI12/02248, FR2009-0052 and IT2009-0053toGV), Comunidad de Madrid (S2011/BMD-2308toMG), Fundacion Mutua Madrilena (AP101042012 to GV) and Breast Cancer Campaign (2012NovSP033 to EKT and GV). Purchase of the TRIB3-deficient mice (LEXKO-1947) linewas fundedby theWellcomeTrust.Tribbles pseudokinase-3 (TRIB3) has been proposed to act as an inhibitor of AKT although the precise molecular basis of this activity and whether the loss of TRIB3 contributes to cancer initiation and progression remain to be clarified. In this study, by using a wide array of in vitro and in vivo approaches, including a Trib3 knockout mouse, we demonstrate that TRIB3 has a tumor- suppressing role. We also find that the mechanism by which TRIB3 loss enhances tumorigenesis relies on the dysregulation of the phosphorylation of AKT by the mTORC2 complex, which leads to an enhanced phosphorylation of AKT on Ser473 and the subsequent hyperphosphorylation and inactivation of the transcription factor FOXO3. These observations support the notion that loss of TRIB3 is associated with a more aggressive phenotype in various types of tumors by enhancing the activity of the mTORC2/AKT/FOXO axisDepto. de Bioquímica y Biología MolecularFac. de Ciencias QuímicasTRUEpu