Search

Major Depressive Disorder (MDD) is a complex neuropsychiatric disease with known genetic associations, but without known links to rare variation in the human genome. Here we aim to identify rare genetic variants associated with MDD using deep whole-genome sequencing data in an independent population.We report the sequencing of 1,688 whole genomes in a large sample of male-male Veteran twins. Depression status was classified based on a structured diagnostic interview according toOur analysis identified one gene associated with severe depression, basic helix loop helix e22 (The gene

NSC243928 induces cell death in triple-negative breast cancer cells in a LY6K-dependent manner. NSC243928 has been reported as an anti-cancer agent in the NCI small molecule library. The molecular mechanism of NSC243928 as an anti-cancer agent in the treatment of tumor growth in the syngeneic mouse model has not been established. With the success of immunotherapies, novel anti-cancer drugs that may elicit an anti-tumor immune response are of high interest in the development of novel drugs to treat solid cancer. Thus, we focused on studying whether NSC243928 may elicit an anti-tumor immune response in the in vivo mammary tumor models of 4T1 and E0771. We observed that NSC243928 induced immunogenic cell death in 4T1 and E0771 cells. Furthermore, NSC243928 mounted an anti-tumor immune response by increasing immune cells such as patrolling monocytes, NKT cells, B1 cells, and decreasing PMN MDSCs in vivo. Further studies are required to understand the exact mechanism of NSC243928 action in inducing an anti-tumor immune response in vivo, which can be used to determine a molecular signature associated with NSC243928 efficacy. NSC243928 may be a good target for future immuno-oncology drug development for breast cancer.

OBJECTIVES Major Depressive Disorder (MDD) is a complex neuropsychiatric disease with known genetic associations, but without known links to rare variation in the human genome. Here we aim to identify rare genetic variants associated with MDD using deep whole-genome sequencing data in an independent population. METHODS We report the sequencing of 1,688 whole genomes in a large sample of male-male Veteran twins. Depression status was classified based on a structured diagnostic interview according to DSM-III-R diagnostic criteria. Searching only rare variants in genomic regions from recent GWAS on MDD, we used the optimised sequence kernel association test and Fisher's Exact test to fine map loci associated with severe depression. RESULTS Our analysis identified one gene associated with severe depression, basic helix loop helix e22 (PAdjusted = 0.03) via SKAT-O test between unrelated severely depressed cases compared to unrelated non-depressed controls. The same gene BHLHE22 had a non-silent variant rs13279074 (PAdjusted = 0.032) based on a single variant Fisher's Exact test between unrelated severely depressed cases compared to unrelated non-depressed controls. CONCLUSION The gene BHLHE22 shows compelling genetic evidence of directly impacting the severe depression phenotype. Together these results advance understanding of the genetic contribution to major depressive disorder in a new cohort and link a rare variant to severe forms of the disorder.

Drug resistance is a constant threat to malaria control efforts making it important to maintain a good pipeline of new drug candidates. Of particular need are compounds that also block transmission...

Hannu Laaksovirta konsortion jäsenenä. The Genomics England Research Consortium, The International ALS/FTD Genomics Consortium (iAFGC), The International FTD Genetics Consortium (IFGC), The International LBD Genomics Consortium (iLBDGC), The NYGC ALS Consortium, The PROSPECT Consortium,17 James B. Rowe,17 Luisa Benussi,18 Giuliano Binetti,18,19 Roberta Ghidoni,18 Edwin Jabbari,20,21 Coralie Viollet,22 Jonathan D. Glass,23 Andrew B. Singleton,24 Vincenzo Silani,25,26 Owen A. Ross,27 Mina Ryten,8,28,29 Ali Torkamani,30 Toshiko Tanaka,31 Luigi Ferrucci,31 Susan M. Resnick,32 We examined the role of repeat expansions in the pathogenesis of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) by analyzing whole-genome sequence data from 2,442 FTD/ALS patients, 2,599 Lewy body dementia (LBD) patients, and 3,158 neurologically healthy subjects. Pathogenic expansions (range, 40?64 CAG repeats) in the huntingtin (HTT) gene were found in three (0.12%) patients diagnosed with pure FTD/ALS syndromes but were not present in the LBD or healthy cohorts. We replicated our findings in an independent collection of 3,674 FTD/ALS patients. Postmortem evaluations of two patients revealed the classical TDP-43 pathology of FTD/ALS, as well as huntingtin-positive, ubiquitin-positive aggregates in the frontal cortex. The neostriatal atrophy that pathologically defines Huntington?s disease was absent in both cases. Our findings reveal an etiological relationship between HTT repeat expansions and FTD/ALS syndromes and indicate that genetic screening of FTD/ALS patients for HTT repeat expansions should be considered. We examined the role of repeat expansions in the pathogenesis of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) by analyzing whole-genome sequence data from 2,442 FTD/ALS patients, 2,599 Lewy body dementia (LBD) patients, and 3,158 neurologically healthy subjects. Pathogenic expansions (range, 40?64 CAG repeats) in the huntingtin (HTT) gene were found in three (0.12%) patients diagnosed with pure FTD/ALS syndromes but were not present in the LBD or healthy cohorts. We replicated our findings in an independent collection of 3,674 FTD/ALS patients. Postmortem evaluations of two patients revealed the classical TDP-43 pathology of FTD/ALS, as well as huntingtin-positive, ubiquitin-positive aggregates in the frontal cortex. The neostriatal atrophy that pathologically defines Huntington?s disease was absent in both cases. Our findings reveal an etiological relationship between HTT repeat expansions and FTD/ALS syndromes and indicate that genetic screening of FTD/ALS patients for HTT repeat expansions should be considered.

[Image: see text] Drug resistance is a constant threat to malaria control efforts making it important to maintain a good pipeline of new drug candidates. Of particular need are compounds that also block transmission by targeting sexual stage parasites. Mature sexual stages are relatively resistant to all currently used antimalarials except the 8-aminoquinolines that are not commonly used due to potential side effects. Here, we synthesized a new Torin 2 derivative, NCATS-SM3710 with increased aqueous solubility and specificity for Plasmodium and demonstrate potent in vivo activity against all P. berghei life cycle stages. NCATS-SM3710 also has low nanomolar EC(50)s against in vitro cultured asexual P. falciparum parasites (0.38 ± 0.04 nM) and late stage gametocytes (5.77 ± 1 nM). Two independent NCATS-SM3710/Torin 2 resistant P. falciparum parasite lines produced by growth in sublethal Torin 2 concentrations both had genetic changes in PF3D7_0509800, annotated as a phosphatidylinositol 4 kinase (Pf PI4KIIIβ). One line had a point mutation in the putative active site (V1357G), and the other line had a duplication of a locus containing Pf PI4KIIIβ. Both lines were also resistant to other Pf PI4K inhibitors. In addition NCATS-SM3710 inhibited purified Pf PI4KIIIβ with an IC(50) of 2.0 ± 0.30 nM. Together the results demonstrate that Pf PI4KIIIβ is the target of Torin 2 and NCATS-SM3710 and provide new options for potent multistage drug development.

CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9)-mediated genome editing holds remarkable promise for the treatment of human genetic diseases. However, the possibility of off-target Cas9 activity remains a concern. To address this issue using clinically relevant target cells, we electroporated Cas9 ribonucleoprotein (RNP) complexes (independently targeted to two different genomic loci, the CXCR4 locus on chromosome 2 and the AAVS1 locus on chromosome 19) into human mobilized peripheral blood-derived hematopoietic stem and progenitor cells (HSPCs) and assessed the acquisition of somatic mutations in an unbiased, genome-wide manner via whole genome sequencing (WGS) of single-cell-derived HSPC clones. Bioinformatic analysis identified &gt, 20,000 total somatic variants (indels, single nucleotide variants, and structural variants) distributed among Cas9-treated and non-Cas9-treated control HSPC clones. Statistical analysis revealed no significant difference in the number of novel non-targeted indels among the samples. Moreover, data analysis showed no evidence of Cas9-mediated indel formation at 623 predicted off-target sites. The median number of novel single nucleotide variants was slightly elevated in Cas9 RNP-recipient sample groups compared to baseline, but did not reach statistical significance. Structural variants were rare and demonstrated no clear causal connection to Cas9-mediated gene editing procedures. We find that the collective somatic mutational burden observed within Cas9 RNP-edited human HSPC clones is indistinguishable from naturally occurring levels of background genetic heterogeneity.

Parasites, defined as eukaryotic microbes and parasitic worms that cause global diseases of human and veterinary importance, span many lineages in the eukaryotic Tree of Life. Historically challenging to study due to their complicated life-cycles and association with impoverished settings, their inherent complexities are now being elucidated by genome sequencing. Over the course of the last decade, projects in large sequencing centers, and increasingly frequently in individual research labs, have sequenced dozens of parasite reference genomes and field isolates from patient populations. This “tsunami” of genomic data is answering questions about parasite genetic diversity, signatures of evolution orchestrated through anti-parasitic drug and host immune pressure, and the characteristics of populations. This brief review focuses on the state of the art of parasitic protist genomics, how the peculiar genomes of parasites are driving creative methods for their sequencing, and the impact that next-generation sequencing is having on our understanding of parasite population genomics and control of the diseases they cause.

Eukaryotes contain short (∼80–200 bp) regions that have few or no substitutions among species that represent hundreds of millions of years of evolutionary divergence. These ultraconserved elements (UCEs) are candidates for containing essential functions, but their biological roles remain largely unknown. Here, we report the discovery and characterization of UCEs from 12 sequenced Drosophila species. We identified 98 elements ≥80 bp long with very high conservation across the Drosophila phylogeny. Population genetic analyses reveal that these UCEs are not present in mutational cold spots. Instead we infer that they experience a level of selective constraint almost 10-fold higher compared with missense mutations in protein-coding sequences, which is substantially higher than that observed previously for human UCEs. About one-half of these Drosophila UCEs overlap the transcribed portion of genes, with many of those that are within coding sequences likely to correspond to sites of ADAR-dependent RNA editing. For the remaining UCEs that are in nongenic regions, we find that many are potentially capable of forming RNA secondary structures. Among ten chosen for further analysis, we discovered that the majority are transcribed in multiple tissues of Drosophila melanogaster. We conclude that Drosophila species are rich with UCEs and that many of them may correspond to novel noncoding RNAs.

Plasmodium vivax is a major public health burden, responsible for the majority of malaria infections outside Africa. We explored the impact of demographic history and selective pressures on the P. vivax genome by sequencing 182 clinical isolates sampled from 11 countries across the globe, using hybrid selection to overcome human DNA contamination. We confirmed previous reports of high genomic diversity in P. vivax relative to the more virulent Plasmodium falciparum species; regional populations of P. vivax exhibited greater diversity than the global P. falciparum population, indicating a large and/or stable population. Signals of natural selection suggest that P. vivax is evolving in response to antimalarial drugs and is adapting to regional differences in the human host and the mosquito vector. These findings underline the variable epidemiology of this parasite species and highlight the breadth of approaches that may be required to eliminate P. vivax globally.

Background Fabric-like hemostatic dressings offer promise for hemorrhage control in noncompressible areas, especially given their similarity in form to standard gauze currently in use. Recently, two such products, Combat Gauze (CBG) and TraumaStat (TMS), were introduced. Their performance is evaluated in two vascular injury models. Materials and Methods The dressings were evaluated in anesthetized Yorkshire pigs, hemorrhaged by full transection of the femoral vasculature with 2 min free bleeding period (CBG = 6, TMS = 6) or by 4 mm femoral arterial puncture with 45 s free bleeding period (CBG = 8, TMS = 8). After injury, dressings were applied, followed by 5 min of manual compression and then 500 mL resuscitation fluid infused over 30 min. Vital signs, blood pressure, and blood loss were recorded throughout the 3-h experiment. Bleeding control was the primary outcome. Results All animals had similar pretreatment mean arterial pressure (MAP) (∼36.5 mmHg); pretreatment blood loss following injury was similar for both dressing groups in the two models [24% ± 8% estimated blood volume (EBV) 2 min after transection and 17% ± 4% EBV 45 s after puncture. Incidence of post-treatment bleeding, primarily occurring after release of manual compression or restoration of blood pressure, was more frequent in the puncture model (17% with both CBG and TMS) than the transection model (57% with CBG versus 75% with TMS). Post-treatment blood loss not controlled by the dressing was 19% ± 22% and 31% ± 17% EBV, for CBG and TMS, respectively. Survival rate was 100% for both dressings in the transection model, and was 88% for CBG and 50% for TMS in the puncture model. Conclusions These findings indicated that CBG and TMS were similarly effective in improving hemostasis. These two fabric-like dressings showed easy application and removal, leaving a clean wound for surgical repair.

RNA interference (RNAi) is quickly emerging as a vital component of genome organization, gene regulation, and immunity in Drosophila and other species. Previous studies have suggested that, as a whole, genes involved in RNAi are under intense positive selection in Drosophila melanogaster. Here, we characterize the extent and patterns of adaptive evolution in 23 known Drosophila RNAi genes, both within D. melanogaster and across the Drosophila phylogeny. We find strong evidence for recurrent protein-coding adaptation at a large number of RNAi genes, particularly those involved in antiviral immunity and defense against transposable elements. We identify specific functional domains involved in direct protein-RNA interactions as particular hotspots of recurrent adaptation in multiple RNAi genes, suggesting that targeted coadaptive arms races may be a general feature of RNAi evolution. Our observations suggest a predictive model of how selective pressures generated by evolutionary arms race scenarios may affect multiple genes across protein interaction networks and other biochemical pathways.

Here, we describe the construction of a phylogenetically deep, whole-genome alignment of 20 flowering plants, along with an analysis of plant genome conservation. Each included angiosperm genome was aligned to a reference genome, Arabidopsis thaliana, using the LASTZ/MULTIZ paradigm and tools from the University of California‐Santa Cruz Genome Browser source code. In addition to the multiple alignment, we created a local genome browser displaying multiple tracks of newly generated genome annotation, as well as annotation sourced from published data of other research groups. An investigation into A. thaliana gene features present in the aligned A. lyrata genome revealed better conservation of start codons, stop codons, and splice sites within our alignments (51% of features from A. thaliana conserved without interruption in A. lyrata) when compared with previous publicly available plant pairwise alignments (34% of features conserved). The detailed view of conservation across angiosperms revealed not only high coding-sequence conservation but also a large set of previously uncharacterized intergenic conservation. From this, we annotated the collection of conserved features, revealing dozens of putative noncoding RNAs, including some with recorded small RNA expression. Comparing conservation between kingdoms revealed a faster decay of vertebrate genome features when compared with angiosperm genomes. Finally, conserved sequences were searched for folding RNA features, including but not limited to noncoding RNA (ncRNA) genes. Among these, we highlight a double hairpin in the 5 0 -untranslated region (5 0 -UTR) of the PRIN2 gene and a putative ncRNA with homology targeting the LAF3 protein.

Ultraconserved elements (UCEs), stretches of DNA that are identical between distantly related species, are enigmatic genomic features whose function is not well understood. First identified and characterized in mammals, UCEs have been proposed to play important roles in gene regulation, RNA processing, and maintaining genome integrity. However, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. We investigated whether there are highly conserved DNA elements without genic function in distantly related plant genomes. We compared the genomes of Arabidopsis thaliana and Vitis vinifera; species that diverged ∼115 million years ago (Mya). We identified 36 highly conserved elements with at least 85% similarity that are longer than 55 bp. Interestingly, these elements exhibit properties similar to mammalian UCEs, such that we named them UCE-like elements (ULEs). ULEs are located in intergenic or intronic regions and are depleted from segmental duplications. Like UCEs, ULEs are under strong purifying selection, suggesting a functional role for these elements. As their mammalian counterparts, ULEs show a sharp drop of A+T content at their borders and are enriched close to genes encoding transcription factors and genes involved in development, the latter showing preferential expression in undifferentiated tissues. By comparing the genomes of Brachypodium distachyon and Oryza sativa, species that diverged ∼50 Mya, we identified a different set of ULEs with similar properties in monocots. The identification of ULEs in plant genomes offers new opportunities to study their possible roles in genome function, integrity, and regulation.

Thromboelastography (TEG) or rotational thromboelastometry (ROTEM) assesses blood viscoelastic properties and clotting kinetics that can be measured by Haemoscope TEG and Pentapharm ROTEM devices using slightly different methodologies. These devices were compared by measuring blood samples associated with various degrees of coagulopathy. Blood samples, collected from swine undergoing three types of severe injury and resuscitation protocol resulting in normal, hypercoagulopathy, and hypocoagulopathy, were assessed with TEG or ROTEM before the surgical procedures, and after injury, fluid resuscitation, and simulated hospital phase. Standard clotting parameters were compared by Student's t-test at a significance of a P value less than 0.05. Regression analysis indicated a positive correlation between TEG and ROTEM for reaction time (R), clotting rate (K), and maximum amplitude (Ma) parameters. With samples of normal coagulation, R (440 +/- 136 vs. 391 +/- 73 s), K (99 +/- 39 vs. 81 +/- 20 s), and Ma (74 +/- 4 vs. 69 +/- 5 mm) were higher, whereas (alpha) (68 +/- 8 vs. 75 +/- 3 mm) was lower with TEG than ROTEM, respectively; a P value is less than 0.05. The magnitude of changes from baseline in hypercoagulable or hypocoagulable samples due to level of injury was equivalent with TEG and ROTEM indicating comparable use of the instruments. However, when samples were extremely hypocoagulopathic due to resuscitation fluid, the TEG values could not be readily determined. Overall, TEG readings were higher than ROTEM readings; this disparity between the two instruments was attenuated with hypercoaguable samples. Both devices yielded similar information regarding the status of coagulation related to trauma. Because of operating characteristics, the same instrument should be used for monitoring the same patient or study.

The study of the three protagonists in malaria-the Plasmodium parasite, the Anopheles mosquito, and the human host-is key to developing methods to control and eventually eliminate the disease. Genomic technologies, including the recent development of next-generation sequencing, enable interrogation of this triangle to an unprecedented level of scrutiny, and promise exciting progress toward real-time epidemiology studies and the study of evolutionary adaptation. We discuss the use of genomics by the International Centers of Excellence for Malaria Research, a network of field sites and laboratories in malaria-endemic countries that undertake cutting-edge research, training, and technology transfer in malarious countries of the world.