HIV-1 infection activates endogenous retroviral promoters regulating antiviral gene expression.

Although endogenous retroviruses (ERVs) are known to harbor cis-regulatory elements, their role in modulating cellular immune responses remains poorly understood. Using an RNA-seq approach, we show that several members of the ERV9 lineage, particularly LTR12C elements, are activated upon HIV-1 infection of primary CD4+ T cells. Intriguingly, HIV-1-induced ERVs harboring transcription start sites are primarily found in the vicinity of immunity genes. For example, HIV-1 infection activates LTR12C elements upstream of the interferon-inducible genes GBP2 and GBP5 that encode for broad-spectrum antiviral factors. Reporter assays demonstrated that these LTR12C elements drive gene expression in primary CD4+ T cells. In line with this, HIV-1 infection triggered the expression of a unique GBP2 transcript variant by activating a cryptic transcription start site within LTR12C. Furthermore, stimulation with HIV-1-induced cytokines increased GBP2 and GBP5 expression in human cells, but not in macaque cells that naturally lack the GBP5 gene and the LTR12C element upstream of GBP2. Finally, our findings suggest that GBP2 and GBP5 have already been active against ancient viral pathogens as they suppress the maturation of the extinct retrovirus HERV-K (HML-2). In summary, our findings uncover how human cells can exploit remnants of once-infectious retroviruses to regulate antiviral gene expression.

The histone H4K20 methyltransferase SUV4-20H1/KMT5B is required for multiciliated cell differentiation in Xenopus.

H4 lysine 20 dimethylation (H4K20me2) is the most abundant histone modification in vertebrate chromatin. It arises from sequential methylation of unmodified histone H4 proteins by the mono-methylating enzyme PR-SET7/KMT5A, followed by conversion to the dimethylated state by SUV4-20H (KMT5B/C) enzymes. We have blocked the deposition of this mark by depleting Xenopus embryos of SUV4-20H1/H2 methyltransferases. In the larval epidermis, this results in a severe loss of cilia in multiciliated cells (MCC), a key component of mucociliary epithelia. MCC precursor cells are correctly specified, amplify centrioles, but ultimately fail in ciliogenesis because of the perturbation of cytoplasmic processes. Genome-wide transcriptome profiling reveals that SUV4-20H1/H2-depleted ectodermal explants preferentially down-regulate the expression of several hundred ciliogenic genes. Further analysis demonstrated that knockdown of SUV4-20H1 alone is sufficient to generate the MCC phenotype and that its catalytic activity is needed for axoneme formation. Overexpression of the H4K20me1-specific histone demethylase PHF8/KDM7B also rescues the ciliogenic defect in a significant manner. Taken together, this indicates that the conversion of H4K20me1 to H4K20me2 by SUV4-20H1 is critical for the formation of cilia tufts.

Dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm.

Silencing of endogenous retroviruses (ERVs) is largely mediated by repressive chromatin modifications H3K9me3 and DNA methylation. On ERVs, these modifications are mainly deposited by the histone methyltransferase Setdb1 and by the maintenance DNA methyltransferase Dnmt1. Knock-out of either Setdb1 or Dnmt1 leads to ERV de-repression in various cell types. However, it is currently not known if H3K9me3 and DNA methylation depend on each other for ERV silencing. Here we show that conditional knock-out of Setdb1 in mouse embryonic endoderm results in ERV de-repression in visceral endoderm (VE) descendants and does not occur in definitive endoderm (DE). Deletion of Setdb1 in VE progenitors results in loss of H3K9me3 and reduced DNA methylation of Intracisternal A-particle (IAP) elements, consistent with up-regulation of this ERV family. In DE, loss of Setdb1 does not affect H3K9me3 nor DNA methylation, suggesting Setdb1-independent pathways for maintaining these modifications. Importantly, Dnmt1 knock-out results in IAP de-repression in both visceral and definitive endoderm cells, while H3K9me3 is unaltered. Thus, our data suggest a dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm cells. Our findings suggest that Setdb1-meditated H3K9me3 is not sufficient for IAP silencing, but rather critical for maintaining high DNA methylation.

Sensorimotor and sensory gating in depression, anxiety, and their comorbidity.

OBJECTIVES: Abnormal attentional and cognitive processes are thought to increase the risk for depression and anxiety. To improve understanding of brain mechanisms of anxiety and depressive disorders and condition of their comorbidity, the study of early attentional processes was provided. METHODS: Participants were patients with depressive (80 s.), anxiety (69 s.), and comorbid (41 s.) disorders, and healthy volunteers (50 s.). Acoustic startle response (ASR) and P50 component of the auditory event-related potential were recorded. RESULTS: In the ASR model decreased startle response amplitude at the left eye in patients with comorbid disorder was found, and ASR latency was lengthened in all clinical groups. Deficit of prepulse inhibition was unique for comorbid disorder, and might be considered as risk of evolution to more serious condition. Reduced prepulse facilitation was revealed in patients with comorbid and anxiety disorders. In P50 suppression paradigm decreased S1 response amplitude was revealed in all clinical groups, P50 latency was prolonged in depressive and comorbid patients, and P50 suppression deficit was observed in depression and anxiety groups. CONCLUSIONS: The obtained results might be useful for development of integrative neural models of comorbidity of anxiety and depression, and elaboration of diagnostic and therapeutic approaches.

Systematic dissection of biases in whole-exome and whole-genome sequencing reveals major determinants of coding sequence coverage.

Advantages and diagnostic effectiveness of the two most widely used resequencing approaches, whole exome (WES) and whole genome (WGS) sequencing, are often debated. WES dominated large-scale resequencing projects because of lower cost and easier data storage and processing. Rapid development of 3rd generation sequencing methods and novel exome sequencing kits predicate the need for a robust statistical framework allowing informative and easy performance comparison of the emerging methods. In our study we developed a set of statistical tools to systematically assess coverage of coding regions provided by several modern WES platforms, as well as PCR-free WGS. We identified a substantial problem in most previously published comparisons which did not account for mappability limitations of short reads. Using regression analysis and simple machine learning, as well as several novel metrics of coverage evenness, we analyzed the contribution from the major determinants of CDS coverage. Contrary to a common view, most of the observed bias in modern WES stems from mappability limitations of short reads and exome probe design rather than sequence composition. We also identified the ~ 500 kb region of human exome that could not be effectively characterized using short read technology and should receive special attention during variant analysis. Using our novel metrics of sequencing coverage, we identified main determinants of WES and WGS performance. Overall, our study points out avenues for improvement of enrichment-based methods and development of novel approaches that would maximize variant discovery at optimal cost.

The potential for bridging of HIV transmission in the Russian Federation: sex risk behaviors and HIV prevalence among drug users (DUs) and their non-DU sex partners.

The HIV epidemic that began in Russia in the mid-1990s has been concentrated mostly among drug users (DUs). Recent evidence of increasing HIV cases among non-DUs attributed to sexual behavior raises potential concern about a more generalized epidemic. The purpose of this analysis is to examine the potential for HIV transmission from DUs to their non-DU sex partners. Analyses are conducted using data collected during 2005-2008 in St. Petersburg, Russia. A total of 631 DUs were recruited into the sample with an HIV prevalence of 45%. A majority (84%) of DUs reported being sexually active in the past 6 months, and the DU status of their sex partners was reported as follows: 54% DU, 40% non-DU, and 6% unknown DU status. In 41% of partnerships with an HIV-negative or unknown status partner not known to be DU (potential bridging partnerships), the last reported intercourse was unprotected. Female DUs with potential bridging partnerships were more likely than male DUs to be younger and report homelessness and to have multiple or new sex partners. Many non-DU sex partners of DUs enrolled in the study reported new sex partners in the past 6 months (66%), unprotected intercourse at last sex (60%), and multiple sex partners in the past 6 months (48%). HIV prevalence in this group was 15% (eight out of 53). The high prevalence of HIV among DUs, their sexual contact with non-DUs, and the high-risk sexual behaviors of this potential bridging population together indicate the real potential for an increasingly generalized epidemic. The degree to which there will be further transmission from non-DU sex partners of DUs who exhibit high levels of sex risk behaviors to other non-DU sex partners deserves further study.

Potential bridges of heterosexual HIV transmission from drug users to the general population in St. Petersburg, Russia: is it easy to be a young female?

The epidemic of HIV in St. Petersburg, which is currently concentrated among injection drug users (IDUs), may be penetrating into the general population. Non-IDUs who have IDU sex partners (SP) could be potential bridges in an expanding epidemic. To investigate potential bridges, we accrued a convenience sample of 288 non-IDUs whose HIV diagnosis was attributed to sexual transmission and we determined the proportion that had IDUs among their SP. Having IDU SP ever (lifetime) and IDU SP in the last year were the key variables for the analysis of potential bridges in this study. The interaction of gender and age was found to be a significant predictor of having lifetime IDU SP (p = 0.006, chi (2) test) and IDU SP in the last year (p = 0.05, chi (2) test): females aged 26 and younger were more likely to have both lifetime IDU SP and IDU SP in the last year. Among the group of young females, 46% reported ever having an IDU SP. Out of young women reporting ever having an IDU SP, 85% also reported at least one lifetime non-IDU SP. Among the females aged 26 or younger, a lower level of education (odds ratio [OR] = 2.7, confidence interval [CI] = 1.1-6.7), being born in St. Petersburg (OR = 2.9, CI = 1.2-7.2), and alcohol use in the last 30 days (OR = 3.5, CI = 1.3-9.6) were significant correlates for ever having had an IDU SP. Urgent efforts are necessary to expand HIV prevention to target the potential bridging population to prevent further transmission.

Whole-exome sequencing provides insights into monogenic disease prevalence in Northwest Russia.

BACKGROUND: Allele frequency data from large exome and genome aggregation projects such as the Genome Aggregation Database (gnomAD) are of ultimate importance to the interpretation of medical resequencing data. However, allele frequencies might significantly differ in poorly studied populations that are underrepresented in large-scale projects, such as the Russian population. METHODS: In this work, we leveraged our access to a large dataset of 694 exome samples to analyze genetic variation in the Northwest Russia. We compared the spectrum of genetic variants to the dbSNP build 151, and made estimates of ClinVar-based autosomal recessive (AR) disease allele prevalence as compared to gnomAD r. 2.1. RESULTS: An estimated 9.3% of discovered variants were not present in dbSNP. We report statistically significant overrepresentation of pathogenic variants for several Mendelian disorders, including phenylketonuria (PAH, rs5030858), Wilson's disease (ATP7B, rs76151636), factor VII deficiency (F7, rs36209567), kyphoscoliosis type of Ehlers-Danlos syndrome (FKBP14, rs542489955), and several other recessive pathologies. We also make primary estimates of monogenic disease incidence in the population, with retinal dystrophy, cystic fibrosis, and phenylketonuria being the most frequent AR pathologies. CONCLUSION: Our observations demonstrate the utility of population-specific allele frequency data to the diagnosis of monogenic disorders using high-throughput technologies.

Transcriptome of the bivalve Limecola balthica L. from Western Pacific: A new resource for studies of European populations.

The Baltic clam Limecola balthica L. (Tellinidae) is broadly used in ecophysiological, toxicological, evolutionary and environmental monitoring studies. However, it is poorly studied in respect of genome and gene functions. We obtained a transcriptome of Limecola b. balthica from Kamchatka (Western Pacific) generated with the use of Illumina high-throughput sequencing. We annotated 11,374 proteins, including 53 from the oxidative phosphorylation pathway and a number of pollution-stress biomarkers, recovered 254,540 single nucleotide variants within two annotated transcriptomes including 25,330 scorable in the previously published European data. Our results confirmed the available allozyme data indicating that nuclear genomes of the clams from the Baltic Sea were intermediate in their genetic composition between the Pacific (L. b. balthica) and the Atlantic (L. b. rubra) subspecies. At the same time, the mitochondrial genomes of Limecola from Kamchatka were nearly identical to the single published genome from the Baltic. The genomic diversity in Limecola was found to be high and comparable with that of other marine mollusks (0.0138 and 0.0142 heterozygous positions in the two studied transcriptomes). The data obtained in our study are a valuable resource for further development of genomic markers for evolutionary genetic and ecophysiological studies of L. balthica complex.

Analytical "bake-off" of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis.

A comparative analysis of whole genome sequencing (WGS) and genotype calling was initiated for ten human genome samples sequenced by St. Petersburg State University Peterhof Sequencing Center and by three commercial sequencing centers outside of Russia. The sequence quality, efficiency of DNA variant and genotype calling were compared with each other and with DNA microarrays for each of ten study subjects. We assessed calling of SNPs, indels, copy number variation, and the speed of WGS throughput promised. Twenty separate QC analyses showed high similarities among the sequence quality and called genotypes. The ten genomes tested by the centers included eight American patients afflicted with autoimmune hepatitis (AIH), plus one case's unaffected parents, in a prelude to discovering genetic influences in this rare disease of unknown etiology. The detailed internal replication and parallel analyses allowed the observation of two of eight AIH cases carrying a rare allele genotype for a previously described AIH-associated gene (FTCD), plus multiple occurrences of known HLA-DRB1 alleles associated with AIH (HLA-DRB1-03:01:01, 13:01:01 and 7:01:01). We also list putative SNVs in other genes as suggestive in AIH influence.

Leukocyte elastase and autoantibodies to nerve growth factor in the acute phase of schizophrenia and their relationship to symptomatology.

Many investigations suggest that abnormalities of the immune system are involved in the pathophysiology of schizophrenia. We recently found increased activity of leukocyte elastase (LE) and elevated levels of autoantibodies to neurospecific protein - nerve growth factor (Aab to NGF) - products of the innate and adaptive arms of the immune system in the serum of patients with acute stage schizophrenia. The aim of this study is to elucidate whether or not the changes of LE activity and Aab to NGF level are related to prominent features of schizophrenia. Patients (n=71) corresponding to ICD-10 criteria for relapse-remitting schizophrenia were assessed by the Positive and Negative Syndrome Scale (PANSS). Patients with predominantly positive symptoms showed significantly elevated serum levels of Aab to NGF compared to patients with predominantly negative symptoms, who were more likely to exhibit the high LE activity. Moreover, progression of positive symptoms was coupled with gradual increase of Aab to NGF level and reduction of LE activity. Based on these findings we conclude that the high levels of Aab to NGF relate to a clinical picture characterised mainly by positive symptoms of schizophrenia, whereas high LE-activities relate to a clinical picture with mainly negative symptoms of schizophrenia.

ß-carboline compounds, including harmine, inhibit DYRK1A and tau phosphorylation at multiple Alzheimer's disease-related sites.

Harmine, a ß-carboline alkaloid, is a high affinity inhibitor of the dual specificity tyrosine phosphorylation regulated kinase 1A (DYRK1A) protein. The DYRK1A gene is located within the Down Syndrome Critical Region (DSCR) on chromosome 21. We and others have implicated DYRK1A in the phosphorylation of tau protein on multiple sites associated with tau pathology in Down Syndrome and in Alzheimer's disease (AD). Pharmacological inhibition of this kinase may provide an opportunity to intervene therapeutically to alter the onset or progression of tau pathology in AD. Here we test the ability of harmine, and numerous additional ß-carboline compounds, to inhibit the DYRK1A dependent phosphorylation of tau protein on serine 396, serine 262/serine 356 (12E8 epitope), and threonine 231 in cell culture assays and in vitro phosphorylation assays. Results demonstrate that the ß-carboline compounds (1) potently reduce the expression of all three phosphorylated forms of tau protein, and (2) inhibit the DYRK1A catalyzed direct phosphorylation of tau protein on serine 396. By assaying several ß-carboline compounds, we define certain chemical groups that modulate the affinity of this class of compounds for inhibition of tau phosphorylation.

3H-Quinazolin-4-ones as a new calcilytic template for the potential treatment of osteoporosis.

Structure-activity relationship studies, focused on identification of the active pharmacophore fragments in a single high-throughput screening calcilytic hit, resulted in the discovery of potent calcium receptor antagonists, substituted 3H-quinazolin-4-ones.

Design, new synthesis, and calcilytic activity of substituted 3H-pyrimidin-4-ones.

Design, new synthesis, structure-activity relationship studies and calcium receptor antagonist (calcilytic) properties of novel 3H-pyrimidin-4-ones are described.