Expression of ERV3-1 in leukocytes of acute myelogenous leukemia patients

Acute myelogenous leukemia (AML) is one of the major hematological malignancies. In the human genome, several have been found to originate from retroviruses, and some of which are involved in the progression of various cancers. Hence, to investigate whether retroviral-like genes are associated with AML development, we conducted a transcriptome sequencing analysis of 12 retroviral-like genes of 150 AML patients and 32 healthy donor samples, of which RNA sequencing data were obtained from public databases. We found high expression of ERV3-1, an envelope gene of endogenous retrovirus group 3 member 1, in all AML patients examined in this study. In particular, blood and bone marrow cells of the myeloid lineage in AML patients, exhibited higher expression of ERV3-1 than those of the monocytic AML lineage. We also examined the protein expression of ERV3-1 by immunohistochemical analysis and found expression of the ERV3-1 protein in all 12 myeloid-phenotype patients and 7 out of 12 monocytic-phenotype patients, with a particular concentration observed at the membrane of some leukemic cells. Transcriptome analysis further suggested that upregulated ERV3-1 expression may be associated with chromosome 8 trisomy as anomaly was found to be more common among the high expression group than the low expression group. However, this finding was not corroborated by the immunohistochemical data. This discrepancy may have been caused, in part, by the small number of samples analyzed in this study. Although the precise associated molecular mechanisms remain unclear, our results suggest that ERV3-1 may be involved in AML development.

Comprehensive genomic analysis reveals dynamic evolution of endogenous retroviruses that code for retroviral-like protein domains

Background

Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections of mammalian germline cells. A large proportion of ERVs lose their open reading frames (ORFs), while others retain them and become exapted by the host species. However, it remains unclear what proportion of ERVs possess ORFs (ERV-ORFs), become transcribed, and serve as candidates for co-opted genes.

Results

We investigated characteristics of 176,401 ERV-ORFs containing retroviral-like protein domains (gag, pro, pol, and env) in 19 mammalian genomes. The fractions of ERVs possessing ORFs were overall small (~ 0.15%) although they varied depending on domain types as well as species. The observed divergence of ERV-ORF from their consensus sequences showed bimodal distributions, suggesting that a large proportion of ERV-ORFs either recently, or anciently, inserted themselves into mammalian genomes. Alternatively, very few ERVs lacking ORFs were found to exhibit similar divergence patterns. To identify candidates for ERV-derived genes, we estimated the ratio of non-synonymous to synonymous substitution rates (dN/dS) for ERV-ORFs in human and non-human mammalian pairs, and found that approximately 42% of the ERV-ORFs showed dN/dS < 1. Further, using functional genomics data including transcriptome sequencing, we determined that approximately 9.7% of these selected ERV-ORFs exhibited transcriptional potential.

Conclusions

These results suggest that purifying selection operates on a certain portion of ERV-ORFs, some of which may correspond to uncharacterized functional genes hidden within mammalian genomes. Together, our analyses suggest that more ERV-ORFs may be co-opted in a host-species specific manner than we currently know, which are likely to have contributed to mammalian evolution and diversification.

A role for gorilla APOBEC3G in shaping lentivirus evolution including transmission to humans

The APOBEC3 deaminases are potent inhibitors of virus replication and barriers to cross-species transmission. For simian immunodeficiency virus (SIV) to transmit to a new primate host, as happened multiple times to seed the ongoing HIV-1 epidemic, the viral infectivity factor (Vif) must be capable of neutralizing the APOBEC3 enzymes of the new host. Although much is known about current interactions of HIV-1 Vif and human APOBEC3s, the evolutionary changes in SIV Vif required for transmission from chimpanzees to gorillas and ultimately to humans are poorly understood. Here, we demonstrate that gorilla APOBEC3G is a factor with the potential to hamper SIV transmission from chimpanzees to gorillas. Gain-of-function experiments using SIVcpzPtt Vif revealed that this barrier could be overcome by a single Vif acidic amino acid substitution (M16E). Moreover, degradation of gorilla APOBEC3F is induced by Vif through a mechanism that is distinct from that of human APOBEC3F. Thus, our findings identify virus adaptations in gorillas that preceded and may have facilitated transmission to humans.

Humans are exposed continuously to a menace of viral diseases such as Ebola virus and coronaviruses. Such emerging/re-emerging viral outbreaks can be triggered by cross-species viral transmission from wild animals to humans. HIV-1, the causative agent of AIDS, most likely originated from related precursors found in chimpanzees and gorillas (SIVcpzPtt or SIVgor), approximately 100 years ago. Additionally, SIVgor most likely emerged through the cross-species jump of SIVcpzPtt from chimpanzees to gorillas. However, it remains unclear how primate lentiviruses successfully transmitted among different species. To limit cross-species lentiviral transmission, cellular "restriction factors", including tetherin, SAMHD1, and APOBEC3 proteins potentially inhibit lentiviral replication. In contrast, primate lentiviruses have evolutionary acquired their own "arms" to antagonize the antiviral effect of restriction factors. Here we show that gorilla APOBEC3G potentially plays a role in inhibiting SIVcpzPtt replication. To our knowledge, this is the first report suggesting that a great ape APOBEC3 protein can potentially restrict the cross-species transmission of great ape lentiviruses and how lentiviruses overcame this species barrier.

SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant

One of the features distinguishing SARS-CoV-2 from its more pathogenic counterpart SARS-CoV is the presence of premature stop codons in its ORF3b gene. Here, we show that SARS-CoV-2 ORF3b is a potent interferon antagonist, suppressing the induction of type I interferon more efficiently than its SARS-CoV ortholog. Phylogenetic analyses and functional assays reveal that SARS-CoV-2-related viruses from bats and pangolins also encode truncated ORF3b gene products with strong anti-interferon activity. Furthermore, analyses of approximately 17,000 SARS-CoV-2 sequences identify a natural variant in which a longer ORF3b reading frame was reconstituted. This variant was isolated from two patients with severe disease and further increased the ability of ORF3b to suppress interferon induction. Thus, our findings not only help to explain the poor interferon response in COVID-19 patients but also describe the emergence of natural SARS-CoV-2 quasispecies with an extended ORF3b gene that may potentially affect COVID-19 pathogenesis.

In-vitro fertilisation-embryo-transfer complicates the antenatal diagnosis of placenta accreta spectrum using MRI: a retrospective analysis

AIM

To evaluate the diagnostic accuracy of magnetic resonance imaging (MRI) for the antenatal diagnosis of placenta accreta spectrum (PAS).

MATERIALS AND METHODS

Data from 95 patients with placenta previa or low-lying placenta who underwent MRI at Osaka University Hospital for the antenatal diagnosis of PAS between January 2013 and December 2018 were reviewed retrospectively. The antenatal MRI signs suggesting PAS were assessed. Patients were divided into two groups depending on whether they were diagnosed with PAS. Factors that affected PAS diagnosis were identified using multivariate analysis.

RESULTS

The diagnostic accuracy of MRI for detecting PAS was as follows: 71.4% sensitivity, 96.4% specificity, and area under the curve (AUC) of 0.839 (95% confidence interval [CI]: 0.73-0.91). The diagnostic accuracy was lower in patients with in-vitro fertilisation with embryo transfer (IVF-ET): 22.2% sensitivity, 93.3% specificity, and AUC=0.578 (95% CI: 0.417-0.724). On multivariate analysis, only IVF-ET showed a significant association with false-positive or -negative MRI diagnosis of PAS (adjusted odds ratio: 26.5; 95% CI: 2.42-289.4; p=0.007).

CONCLUSION

IVF-ET affects the antenatal diagnosis of PAS using MRI.

Genome evolution of SARS-CoV-2 and its virological characteristics

Coronavirus disease of 2019 (COVID-19), which originated in China in 2019, shows mild cold and pneumonia symptoms that can occasionally worsen and result in deaths. SARS-CoV-2 was reported to be the causative agent of the disease and was identified as being similar to SARS-CoV, a causative agent of SARS in 2003. In this review, we described the phylogeny of SARS-CoV-2, covering various related studies, in particular, focusing on viruses obtained from horseshoe bats and pangolins that belong to Sarbecovirus, a subgenus of Betacoronavirus. We also describe the virological characteristics of SARS-CoV-2 and compare them with other coronaviruses. More than 30,000 genome sequences of SARS-CoV-2 are available in the GISAID database as of May 28, 2020. Using the genome sequence data of closely related viruses, the genomic characteristics and evolution of SARS-CoV-2 were extensively studied. However, given the global prevalence of COVID-19 and the large number of associated deaths, further computational and experimental virological analyses are required to fully characterize SARS-CoV-2.

A high-throughput detection method for the clonality of Human T-cell leukemia virus type-1-infected cells in vivo

Approximately 10-20 million of Human T-cell leukemia virus type-1 (HTLV-1)-infected carriers have been previously reported, and approximately 5% of these carriers develop adult T-cell leukemia/lymphoma (ATL) with a characteristic poor prognosis. In Japan, Southern blotting has long been routinely performed for detection of clonally expanded ATL cells in vivo, and as a confirmatory diagnostic test for ATL. However, alternative methods to Southern blotting, such as sensitive, quantitative, and rapid analytical methods, are currently required in clinical practice. In this study, we developed a high-throughput method called rapid amplification of integration site (RAIS) that could amplify HTLV-1-integrated fragments within 4 h and detect the integration sites in > 0.16% of infected cells. Furthermore, we established a novel quantification method for HTLV-1 clonality using Sanger sequencing with RAIS products, and the validity of the quantification method was confirmed by comparing it with next-generation sequencing in terms of the clonality. Thus, we believe that RAIS has a high potential for use as an alternative routine molecular confirmatory test for the clonality analysis of HTLV-1-infected cells.

Nucleotide Archival Format (NAF) enables efficient lossless reference-free compression of DNA sequences

Summary

DNA sequence databases use compression such as gzip to reduce the required storage space and network transmission time. We describe Nucleotide Archival Format (NAF)—a new file format for lossless reference-free compression of FASTA and FASTQ-formatted nucleotide sequences. Nucleotide Archival Format compression ratio is comparable to the best DNA compressors, while providing dramatically faster decompression. We compared our format with DNA compressors: DELIMINATE and MFCompress, and with general purpose compressors: gzip, bzip2, xz, brotli and zstd.

Availability and implementation

NAF compressor and decompressor, as well as format specification are available at https://github.com/KirillKryukov/naf. Format specification is in public domain. Compressor and decompressor are open source under the zlib/libpng license, free for nearly any use.

Supplementary information

Supplementary data are available at Bioinformatics online.

Phylogeny and morphology of new species of Globisporangium

An isolate originally obtained from pond water in Osaka in 1992 and identified as Pythium marsipium, was subsequently classified as Globisporangium marsipium. According to molecular phylogenetic analyses based on the internal transcribed spacer regions of the nuclear ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1 genes, this isolate was shown to represent a new species, described here as G. lacustre sp. nov. In addition, two further new combinations are introduced in Globisporangium as G. camurandrum and G. takayamanum based on their DNA phylogeny.

Efficient differentiation and polarization of primary cultured neurons on poly(lactic acid) scaffolds with microgrooved structures

Synthetic biodegradable polymers including poly(lactic acid) (PLA) are attractive cell culture substrates because their surfaces can be micropatterned to support cell adhesion. The cell adhesion properties of a scaffold mainly depend on its surface chemical and structural features; however, it remains unclear how these characteristics affect the growth and differentiation of cultured cells or their gene expression. In this study, we fabricated two differently structured PLA nanosheets: flat and microgrooved. We assessed the growth and differentiation of mouse primary cultured cortical neurons on these two types of nanosheets after pre-coating with poly-D-lysine and vitronectin. Interestingly, prominent neurite bundles were formed along the grooves on the microgrooved nanosheets, whereas thin and randomly extended neurites were only observed on the flat nanosheets. Comparative RNA sequencing analyses revealed that the expression of genes related to postsynaptic density, dendritic shafts, and asymmetric synapses was significantly and consistently up-regulated in cells cultured on the microgrooved nanosheets when compared with those cultured on the flat nanosheets. These results indicate that microgrooved PLA nanosheets can provide a powerful means of establishing a culture system for the efficient and reproducible differentiation of neurons, which will facilitate future investigations of the molecular mechanisms underlying the pathogenesis of neurological disorders.

Usefulness of next-generation DNA sequencing for the diagnosis of urinary tract infection

Acute urinary tract infection (UTI) is a highly common clinical condition. Although bacterial culture is the gold standard diagnostic test, false negative results may be possible, leading to the pathogen being unidentified. In recent years, bacterial DNA sequencing analysis has garnered much attention, but clinical studies are rare in Japan. In this study, we assessed the usefulness of next-generation DNA sequencing (NGS) analysis for acute UTI patients. We thus performed an observational, retrospective case series study. Urine and blood samples were collected from ten acute UTI patients, of whom four had also been diagnosed with urosepsis. Seven variable regions of bacterial 16S rRNA genes were amplified by PCR and then sequenced by IonPGM. The identified bacterial species were compared with those identified using the culture tests and the clinical parameters were analyzed. As a result, the NGS method effectively identified predominant culture-positive bacteria in urine samples. The urine NGS also detected several culture-negative species, which have been reported to be potentially pathogenic. Out of four urosepsis cases, three were pathogen-positive in blood NGS results, while two were pathogen-negative in blood culture. In one sepsis case, although blood culture was negative for Escherichia coli, this species was detected by blood NGS. For non-sepsis cases, however, blood NGS, as well as blood culture, was less effective in detecting bacterial signals. In conclusion, NGS is potentially useful for identifying pathogenic bacteria in urine from acute UTI patients but is less applicable in patients who do not meet clinical criteria for sepsis.

Phylogenetic analyses reveal that simian foamy virus isolated from Japanese Yakushima macaques (Macaca fuscata yakui) is distinct from most of Japanese Hondo macaques (Macaca fuscata fuscata)

Japanese macaque (Macaca fuscata) is an indigenous Old World monkey (OWM) species that inhabits the Japanese archipelago. There are two subspecies of Japanese macaque: Yakushima macaque (M. f. yakui) which inhabits Yakushima Island exclusively, and Hondo macaque (M. f. fuscata) which inhabits the mainland of Japan. Yakushima macaque is considered to be branched off from a certain parental macaque group that had inhabited the mainland of Japan. However, the process of sub-speciation of the Yakushima macaque is still unclear at present. In this study, to gain new insight into the process of sub-speciation of Japanese macaque, we utilized the simian foamy virus (SFV) as a marker. SFVs are found in virtually all primates except humans and undergo species-specific cospeciation with the hosts. The phylogenetic analysis of conserved regions of the env gene in SFVs remarkably resembled that of the OWMs with high statistical confidence. The phylogenetic analyses also indicated that there are four (1-4) genotypes among Asian OWMs investigated. SFVs derived from Asian OWMs except Yakushima macaque were classified as genotypes 1-3, whereas SFVs isolated from all Yakushima macaques and one Hondo macaque were classified as genotype 4. Interestingly, genotype 4 was firstly branched off from the rest of the genotypes, which might indicate that the macaques infected with genotype 4 SFV were derived from the "older" population of Japanese macaques. The high prevalence of genotype 4 SFVs among Yakushima macaque might reflect the possibility that they are a descendant of the population settled earlier, which has been geographically isolated in Yakushima Island.

The clinical impact of preoperative body composition differs between male and female colorectal cancer patients

AIM

Patient body composition is an important indicator of metabolic status and is associated with cancer progression. Because body composition varies between men and women, we aimed to examine the difference in clinical impact of preoperative body composition according to sex.

METHOD

We used an integrated dataset of 559 colorectal cancer (CRC) patients. The association between preoperative body composition indices [body mass index (BMI), visceral to subcutaneous fat area ratio (VSR) and skeletal muscle index (SMI)] and patient outcome, clinicopathological factors and preoperative inflammation and nutritional status was analysed, comparing men and women.

RESULTS

Preoperative low BMI and low SMI in men was significantly associated with unfavourable overall survival (OS) [BMI: hazard ratio (HR) 2.22, 95% CI 1.28-4.14, P = 0.004; SMI: HR 2.54, 95% CI 1.61-4.07, P < 0.001] and high VSR in women was significantly associated with unfavourable OS (HR 1.79, 95% CI 1.03-3.02, P = 0.040). Additionally, low SMI in men was significantly associated with deeper tumour invasion and greater distant metastasis and high VSR in women was significantly associated with advanced age, right-sided tumour, lower total lymphocyte count and lower albumin levels. Interestingly, low BMI in men was significantly associated with deeper tumour invasion, but also with favourable inflammation and nutritional status (lower C-reactive protein and higher albumin).

CONCLUSION

The clinical impact of preoperative body composition differed between men and women: SMI in men and VSR in women were good prognosticators. Our findings may provide a novel insight for CRC treatment strategies.

Polymer gel with a flexible and highly ordered three-dimensional network synthesized via bond percolation

Gels are a soft elastic material consisting of a three-dimensional polymer network with nanometer-sized pores and are used in a variety of applications. However, gel networks typically have a substantial level of defects because the network formation reaction proceeds stochastically. In this study, we present a general scheme to fabricate gels with extremely low levels of defects by applying geometric constraints into pregel solution based on the "bond percolation" concept. In the formed gel, stationary laser speckles, which are an indicator of spatial defects, were not observed at all. In addition, we found that the concentration fluctuations of the polymer chains were ergodic across the whole gel network. In such a homogeneous gel, both the spatial and temporal correlations of polymer chains are the same before and after gelation.

Rapid sequencing-based diagnosis of infectious bacterial species from meningitis patients in Zambia

OBJECTIVES

We have developed a portable system for the rapid determination of bacterial composition for the diagnosis of infectious diseases. Our system comprises of a nanopore technology-based sequencer, MinION, and two laptop computers. To examine the accuracy and time efficiency of our system, we provided a proof-of-concept for the detection of the causative bacteria of 11 meningitis patients in Zambia.

METHODS

We extracted DNA from cerebrospinal fluid samples of each patient and amplified the 16S rRNA gene regions. The sequencing library was prepared, and the sequenced reads were simultaneously processed for bacterial composition determination using the minimap2 software and the representative prokaryote genomes.

RESULTS

The sequencing results of four of the six culture-positive samples were consistent with those of conventional culture-based methods. The dominant bacterial species in each of these samples were identified from the sequencing data within only 3 min. Although the major bacterial species were also detected from the other two culture-positive samples and five culture-negative samples, their presence could not be confirmed. Moreover, as a whole, although the number of sequencing reads obtained within a short sequencing run was small, there was no change in the major bacterial species over time with prolonged sequencing. In addition, the processing time strongly correlated with the number of sequencing reads used for the analysis.

CONCLUSION

Our results suggest that time-effective analysis could be achieved by determining the number of sequencing reads required for the rapid diagnosis of infectious bacterial species depending on the complexity of bacterial species in a sample.

Human short tandem repeat identification using a nanopore-based DNA sequencer: a pilot study

Short tandem repeats (STRs) are repetitive DNA sequences that are highly polymorphic and widely used for personal identification in the field of forensic medicine. The standard method for determining the repeat number of STRs is capillary electrophoresis of PCR products; however, the use of DNA sequencing has increased because it can identify same-sized alleles with nucleotide substitutions (iso-alleles). In this study, we performed human STR genotyping using a portable nanopore-based DNA sequencer, the MinION, and evaluated its performance. Because the sequence quality obtained by MinION is considerably lower than those obtained with other DNA sequencers, we developed an original scoring scheme for judging the genotypes from MinION reads. Analysis of seven human samples for 21-45 STR loci yielded an average of 857 thousand reads per sample, and the accuracy of genotyping and iso-allele identification reached 75.7% and 82%, respectively. Although the accuracy is higher than that reported previously, further improvements are required before this method can be practically applied.

P684Long-term outcomes in patients with cancer undergoing percutaneous coronary intervention: analysis from a Japan multicenter registry

Background

Cancer and cardiovascular disease (CVD) is the most common cause of death in developed countries, and substantial overlap exist in their medical care. However, the detailed and updated information on outcome of cancer patients with cardiovascular disease (CVD), particularly in clinically significant coronary artery disease (CAD) remain unknown.

Purpose

We sought to describe the prevalence and long-term outcomes of cancer patients undergoing percutaneous coronary intervention (PCI), which has become a coronerstone in the management of CVD.

Methods

Patient data extracted from a regional prospectiveprocedure-based multicenter registry for PCI was analyzed. A total of 4,455 patients who underwent PCI at 15 hospitals within metropolitan Tokyo from September 2008 to 2012 were followed for 2 years. “Active” cancer patient was defined as having a history of cancer not cured or in remission. We analyzed in acute and stable presentation.The occurrence of clinical outcomes was assessed via Kaplan-Meier survival curve, and Cox-regression hazard model to adjust for known clinical predictors.

Results

Within the studied patients, 173 (3.9%) had a concomitant “active” cancer at the time of intervention. There was a significant difference between the patients with and without active cancer in each situation. In stable presentation, cancer group were older, lower BMI, frequently had silent ischemia, COPD and cerebrovascular/peripheral disease, and less often had dyslipidemia compared with non-cancer group. In acute presentation, cancer group were older, frequently had COPD, CKD, peripheral disease and history of HF compared with non-cancer group. The prescription rate of RAAS inhibitor was lower in the cancer group than in the non-cancer group in acute presentation. Notably, in both acute and stable presentation, these patients had significantly higher risk of all-cause mortality (HR 8.01: 95%, p<0.001 and HR5.53: 95%, p<0.001, respectively), and they were also at higher risk of major cardo- and cerebrovascular events (MACCE; HR2.38, p<0.001, HR2.33, p=0.001), when referenced to non-cancer patients after 2 year of follow-up.

Conclusion

Cancer patient was present in 3.9% of all PCI patients and was strongly associated with both non-cardiac and cardiac adverse events.

P5551Comparison of prognostic predictors of heart failure admission and progression to end-stage in hypertrophic cardiomyopathy

Background

Heart failure (HF) is a common complication within the clinical spectrum of hypertrophic cardiomyopathy (HCM). HCM-related HF is recognized to be multifactorial, including outflow obstruction, diastolic dysfunction, or progression to end-stage; however, prognostic predictors of HF events are not fully understood. We sought to investigate predictors for various HF outcomes in HCM.

Methods

We studied 289 consecutive HCM patients with EF≥50%. Patients with outflow obstruction (peak pressure gradient ≥30mmHg) were defined as obstructive HCM. HF events assessed in this study were 1) HF admission and 2) progression to end-stage (EF<50%).

Results

The mean age was 63±16 years, 53% male, EF 61±5%, NYHA class 1.8±0.7, and 39% obstructive. During a median follow up of 5.2 [3.7–7.0] years, 48 HF admission and 19 progression to end-stage were observed. Only 8/48 (17%) patients with HF admission had progressed to end-stage; while 11/19 (58%) patients with progression to end-stage remained free from HF admission. Univariate Cox regression hazard analysis showed different prognostic predictors between HF admission and progression to end-stage (Table). Multivariate Cox regression hazard analysis showed atrial fibrillation was an independent predictor of HF admission (adjusted HR 2.711 [1.094–7.389], P=0.031); while LV end-systolic dimension was an independent predictor of progression to end-stage (adjusted HR 1.114 [1.018–1.229], P=0.025).

Cox hazard analysis for predicting event HF admission Progression to end-stage HR (95% CI) P value HR (95% CI) P value Age, 1 year 1.042 (1.017–1.071) <0.001 1.002 (0.975–1.035) 0.89 Male sex 1.052 (0.595–1.882) 0.86 2.853 (1.034–10.02) 0.043 Atrial fibrillation 3.247 (1.809–6.608) <0.001 1.434 (0.570–3.559) 0.44 Non-obstructive 0.850 (0.481–1.531) 0.58 5.439 (1.558–34.30) 0.005 LV end-diastolic dimension, 1mm 1.027 (0.981–1.077) 0.25 1.120 (1.035–1.218) 0.005 LV end-systolic dimension, 1mm 1.059 (1.008–1.110) 0.023 1.167 (1.080–1.258) <0.001 EF, 1% 0.974 (0.926–1.032) 0.36 0.894 (0.825–0.980) 0.018 LA volume, 1ml/m2 1.012 (1.001–1.020) 0.044 1.006 (0.978–1.023) 0.64 Transmitral E wave, 1m/s 1.013 (1.002–1.024) 0.025 1.006 (0.987–1.023) 0.50 Transmitral DcT, 1msec 0.999 (0.995–1.003) 0.59 0.985 (0.974–0.994) <0.001 E/e', 1.0 1.062 (1.012–1.109) 0.015 1.089 (1.010–1.164) 0.027

Conclusions

Different prognostic predictors were found for HF admission and progression to end-stage, suggesting the difficulty and multifactorial nature of HCM-related HF.

P5393Deficiency of the long noncoding RNA NEAT1 disturbs T cell and monocyte-macrophage lineage differentiation and functions and results in systemic inflammation with high circulating interferon levels

Background

Inflammation is a key driver of atherosclerosis and myocardial infarction (MI), and beyond proteins and microRNAs, long noncoding RNAs (lncRNAs) are implicated in inflammation control. To obtain further information on the role of lncRNAs in the context of atherosclerosis, we analyzed transcriptome maps of circulating immune cells (PBMCs) of post-MI patients in whom the lncRNA NEAT1 was suppressed. Here, we report immune disturbances in murine NEAT1 knockout models with wildtype or ApoE−/− genetic background.

Methods and results

RNA-sequencing (RNA-seq) of PBMCs from post-MI patients revealed profound transcriptome disturbances compared to healthy controls. Among these, NEAT1 suppression was notable since it affected the most highly expressed lncRNA as part of a molecular circuit also encompassing chemokines and interleukins.

We used NEAT1−/− mice to evaluate whether NEAT1 depletion per se may cause immune dysfunction. NEAT1−/− splenocytes displayed enhanced baseline ROS production, and RNA-seq identified anomalous expression and regulation of chemokines/ receptors, innate immunity genes, TNF and caspases. FACS revealed displayed anomalous Treg and TH cell differentiation in NEAT1−/− spleens vs. wildtype (WT).

Beyond grossly altered transcriptome, NEAT1−/− bone marrow derived macrophages (BMDMs) responded to LPS with increased (p<0.001) ROS production, enhanced baseline phagocytic activity (p<0.001), and attenuated proliferation (p=0.001). FACS revealed deregulated monocyte-macrophage differentiation in NEAT1−/− bone marrow and blood.

Further, NEAT1−/− mice displayed aortic wall CD68+ cell infiltration and there was evidence of myocardial inflammation which could lead to severe and potentially life-threatening structural damage in some of these animals. This observation suggests that even stochastic activation of the highly unstable NEAT1−/− immune system may trigger uncontrolled pathogenic cascades, explaining the survival disadvantage of NEAT1−/− mice.

In addition to these studies on homozygous NEAT1−/− deficiency in WT background, we obtained data on mice with partial i.e. heterozygous NEAT1−/+ deficiency on ApoE−/− background. Analysis of this new NEAT1−/+ ApoE−/− strain indicates that even partial NEAT1 deficiency leads to systemic inflammation with high IFN-gamma levels, when the animals are exposed to immune stress e.g. high LDL cholesterol.

Conclusions

Regarding the monocyte-enriched NEAT1 suppressed in post-MI PBMCs, the data from NEAT1−/− and NEAT1−/+ ApoE−/− mice document NEAT1 as a key immune system coordinator whose deficiency affects monocyte-macrophage and T cell differentiation and functions and renders the immune system unstable and highly vulnerable to immune stress. Since in patients NEAT1 is part of a molecular circuit persistently deregulated post-MI, too, it appears reasonable to further search for new therapeutic targets within this circuit, taking advantage of the described genetic animal models.

Identification of a distinct lineage of aviadenovirus from crane feces

Viruses are believed to be ubiquitous; however, the diversity of viruses is largely unknown because of the bias of previous research toward pathogenic viruses. Deep sequencing is a promising and unbiased approach to detect viruses from animal-derived materials. Although cranes are known to be infected by several viruses such as influenza A viruses, previous studies targeted limited species of viruses, and thus viruses that infect cranes have not been extensively studied. In this study, we collected crane fecal samples in the Izumi plain in Japan, which is an overwintering site for cranes, and performed metagenomic shotgun sequencing analyses. We detected aviadenovirus-like sequences in the fecal samples and tentatively named the discovered virus crane-associated adenovirus 1 (CrAdV-1). We determined that our sequence accounted for approximately three-fourths of the estimated CrAdV-1 genome size (33,245 bp). The GC content of CrAdV-1 genome is 34.1%, which is considerably lower than that of other aviadenoviruses. Phylogenetic analyses revealed that CrAdV-1 clusters with members of the genus Aviadenovirus, but is distantly related to the previously identified aviadenoviruses. The protein sequence divergence between the DNA polymerase of CrAdV-1 and those of other aviadenoviruses is 45.2-46.8%. Based on these results and the species demarcation for the family Adenoviridae, we propose that CrAdV-1 be classified as a new species in the genus Aviadenovirus. Results of this study contribute to a deeper understanding of the diversity and evolution of viruses and provide additional information on viruses that infect cranes, which might lead to protection of the endangered species of cranes.