Inference of selective forces on house mouse genomes during secondary contact in East Asia

The house mouse (Mus musculus), which is commensal to humans, has spread globally via human activities, leading to secondary contact between genetically divergent subspecies. This pattern of genetic admixture can provide insights into the selective forces at play in this well-studied model organism. Our analysis of 163 house mouse genomes, with a particular focus on East Asia, revealed substantial admixture between the subspecies castaneus and musculus, particularly in Japan and southern China. We revealed, despite the different level of autosomal admixture among regions, that all Y Chromosomes in the East Asian samples belonged to the musculus-type haplogroup, potentially explained by genomic conflict under sex-ratio distortion owing to varying copy numbers of ampliconic genes on sex chromosomes, Slx and Sly Our computer simulations, designed to replicate the observed scenario, show that the preferential fixation of musculus-type Y Chromosomes can be achieved with a slight increase in the male-to-female birth ratio. We also investigated the influence of selection on the posthybridization of the subspecies castaneus and musculus in Japan. Even though the genetic background of most Japanese samples closely resembles the subspecies musculus, certain genomic regions overrepresented the castaneus-like genetic components, particularly in immune-related genes. Furthermore, a large genomic block (∼2 Mbp) containing a vomeronasal/olfactory receptor gene cluster predominantly harbored castaneus-type haplotypes in the Japanese samples, highlighting the crucial role of olfaction-based recognition in shaping hybrid genomes.

Current trends in RNA virus detection through metatranscriptome sequencing data

With advances in sequencing technology, metatranscriptome sequencing from a variety of environmental and biological sources has revealed the existence of various previously unknown RNA viruses. This review presents recent major RNA virome studies sampled from invertebrate and vertebrate species as well as aquatic environments. In particular, we focus on severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and related RNA virus identification through metatranscriptome sequencing analyses. Recently developed bioinformatics software and databases for RNA virus identification are introduced. A relationship between newly identified RNA viruses and endogenous viral elements in host genomes is also discussed.

Multi-Omics and Artificial Intelligence-Guided Drug Repositioning: Prospects, Challenges, and Lessons Learned from COVID-19

Drug repurposing is of interest for therapeutics innovation in many human diseases including coronavirus disease 2019 (COVID-19). Methodological innovations in drug repurposing are currently being empowered by convergence of omics systems science and digital transformation of life sciences. This expert review article offers a systematic summary of the application of artificial intelligence (AI), particularly machine learning (ML), to drug repurposing and classifies and introduces the common clustering, dimensionality reduction, and other methods. We highlight, as a present-day high-profile example, the involvement of AI/ML-based drug discovery in the COVID-19 pandemic and discuss the collection and sharing of diverse data types, and the possible futures awaiting drug repurposing in an era of AI/ML and digital technologies. The article provides new insights on convergence of multi-omics and AI-based drug repurposing. We conclude with reflections on the various pathways to expedite innovation in drug development through drug repurposing for prompt responses to the current COVID-19 pandemic and future ecological crises in the 21st century.

A New Approach to Drug Repurposing with Two-Stage Prediction, Machine Learning, and Unsupervised Clustering of Gene Expression

Drug repurposing has broad importance in planetary health for therapeutics innovation in infectious diseases as well as common or rare chronic human diseases. Drug repurposing has also proved important to develop interventions against the COVID-19 pandemic. We propose a new approach for drug repurposing involving two-stage prediction and machine learning. First, diseases are clustered by gene expression on the premise that similar patterns of altered gene expression imply critical pathways shared in different disease conditions. Next, drug efficacy is assessed by the reversibility of abnormal gene expression, and results are clustered to identify repurposing targets. To cluster similar diseases, gene expression data from 262 cases of 31 diseases and 268 controls were analyzed by Uniform Manifold Approximation and Projection for Dimension Reduction followed by k-means to optimize the number of clusters. For evaluation, we examined disease-specific gene expression data for inclusion, body myositis, polymyositis, and dermatomyositis (DM), and used LINCS L1000 characteristic direction signatures search engine (L1000CDS2) to obtain lists of small-molecule compounds that reversed the expression patterns of these specifically altered genes as candidates for drug repurposing. Finally, the functions of affected genes were analyzed by Gene Set Enrichment Analysis to examine consistency with expected drug efficacy. Consequently, we found disease-specific gene expression, and importantly, identified 20 drugs such as BMS-387032, phorbol-12-myristate-13-acetate, mitoxantrone, alvocidib, and vorinostat as candidates for repurposing. These were previously noted to be effective against two of the three diseases, and have a high probability of being effective against the other. That is, inclusion body myositis and DM. The two-stage prediction approach to drug repurposing presented here offers innovation to inform future drug discovery and clinical trials in a variety of human diseases.

Whole-Genome Sequencing of Vero E6 (VERO C1008) and Comparative Analysis of Four Vero Cell Sublines

The Vero cell line is an immortalized cell line established from kidney epithelial cells of the African green monkey. A variety of Vero sublines have been developed and can be classified into four major cell lineages. In this study, we determined the whole-genome sequence of Vero E6 (VERO C1008), which is one of the most widely used cell lines for the proliferation and isolation of severe acute respiratory syndrome coronaviruses (SARS-CoVs), and performed comparative analysis among Vero JCRB0111, Vero CCL-81, Vero 76, and Vero E6. Analysis of the copy number changes and loss of heterozygosity revealed that these four sublines share a large deletion and loss of heterozygosity on chromosome 12, which harbors type I interferon and CDKN2 gene clusters. We identified a substantial number of genetic differences among the sublines including single nucleotide variants, indels, and copy number variations. The spectrum of single nucleotide variants indicated a close genetic relationship between Vero JCRB0111 and Vero CCL-81, and between Vero 76 and Vero E6, and a considerable genetic gap between the former two and the latter two lines. In contrast, we confirmed the pattern of genomic integration sites of simian endogenous retroviral sequences, which was consistent among the sublines. We identified subline-specific/enriched loss of function and missense variants, which potentially contribute to the differences in response to viral infection among the Vero sublines. In particular, we identified four genes (IL1RAP, TRIM25, RB1CC1, and ATG2A) that contained missense variants specific or enriched in Vero E6. In addition, we found that V739I variants of ACE2, which functions as the receptor for SARS-CoVs, were heterozygous in Vero JCRB0111, Vero CCL-81, and Vero 76; however, Vero E6 harbored only the allele with isoleucine, resulting from the loss of one of the X chromosomes.

Identification of Characteristic Genomic Markers in Human Hepatoma HuH-7 and Huh7.5.1-8 Cell Lines

The human hepatoma-derived HuH-7 cell line and its derivatives (Huh7.5 and Huh7.5.1) have been widely used as a convenient experimental substitute for primary hepatocytes. In particular, these cell lines represent host cells suitable for propagating the hepatitis C virus (HCV) in vitro. The Huh7.5.1-8 cell line, a subline of Huh7.5.1, can propagate HCV more efficiently than its parental cells. To provide genomic information for cells' quality control, we performed whole-genome sequencing of HuH-7 and Huh7.5.1-8 and identified their characteristic genomic deletions, some of which are applicable to an in-house test for cell authentication. Among the genes related to HCV infection and replication, 53 genes were found to carry missense or loss-of-function mutations likely specific to the HuH-7 and/or Huh7.5.1-8. Eight genes, including DDX58 (RIG-I), BAX, EP300, and SPP1 (osteopontin), contained mutations observed only in Huh7.5.1-8 or mutations with higher frequency in Huh7.5.1-8. These mutations might be relevant to phenotypic differences between the two cell lines and may also serve as genetic markers to distinguish Huh7.5.1-8 cells from the ancestral HuH-7 cells.

Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes

Upstream open reading frames (uORFs) are present in the 5′-untranslated regions of many eukaryotic mRNAs, and some peptides encoded by these regions play important regulatory roles in controlling main ORF (mORF) translation. We previously developed a novel pipeline, ESUCA, to comprehensively identify plant uORFs encoding functional peptides, based on genome-wide identification of uORFs with conserved peptide sequences (CPuORFs). Here, we applied ESUCA to diverse animal genomes, because animal CPuORFs have been identified only by comparing uORF sequences between a limited number of species, and how many previously identified CPuORFs encode regulatory peptides is unclear. By using ESUCA, 1517 (1373 novel and 144 known) CPuORFs were extracted from four evolutionarily divergent animal genomes. We examined the effects of 17 human CPuORFs on mORF translation using transient expression assays. Through these analyses, we identified seven novel regulatory CPuORFs that repressed mORF translation in a sequence-dependent manner, including one conserved only among Eutheria. We discovered a much higher number of animal CPuORFs than previously identified. Since most human CPuORFs identified in this study are conserved across a wide range of Eutheria or a wider taxonomic range, many CPuORFs encoding regulatory peptides are expected to be found in the identified CPuORFs.

THU0225 INTEGRATIVE PLASMA METABOLOME AND TRANSCRIPTOME ANALYSIS REVEALED THE IMPORTANCE OF HISTIDINE HOMEOSTASIS IN SLE PATHOGENESIS WITH POTENTIAL FOR IMPROVED SLE PATIENTS STRATIFICATION

Background:

Recently, immunometabolism has gathered attention of many immunologists. It has been widely recognized that metabolic reprogramming in each immune cell brings different effects on different cells and is important for regulating their functions. Along with the progress of statistical genetics, serum metabolites were shown to be under genetic regulations1). Metabolic changes are now considered not only to be mere phenotypes of cells but also to be key factors for controlling immune cell differentiation, proliferation and function through regulating gene expressions eventually. Although genome-wide association studies have brought deep insights into SLE pathogenesis, the precise pathway from genome to metabolome has been largely unknown, and vice versa.

Objectives:

The aim of this study is to investigate metabolomic regulation in SLE in relation to gene expressions by integrating plasma metabolome data and transcriptome data.

Methods:

We collected plasma samples from patients with SLE (n=57) who met the 1997 American College of Rheumatology criteria for SLE. Gender- and age-matched healthy controls (HCs) (n=56) were recruited. Metabolic profiles focusing on 39 amino acids were analyzed with liquid chromatography (LC)-mass spectrometry. Transcriptome data of SLE patients were obtained from our RNA-sequencing data of each immune cell subset (total 19 subsets). Whole-genome sequencing was also performed.

Results:

Our previous experiment showed that about 160 peaks were detected from comprehensive LC-TOFMS and amino acids were useful for distinguishing SLE patients from HCs. Both partial least squares discriminant analysis (PLS-DA) and random forest, a machine learning algorithm, revealed the importance of histidine (His), one of the essential amino acids, to classify SLE patients from HCs, whose plasma level was lower in SLE patients. In addition, inverse correlation between His level and titer of ds-DNA as well as damage index (SDI) was detected. His level was correlated neither with PSL dosage nor with type I interferon (IFN) signature. Receiver operating characteristic (ROC) analysis showed the best predictability for SLE with the combination of specific amino acids including His. Our transcriptome analysis has revealed the significance of oxidative phosphorylation (OXPHOS) in B cells for SLE pathogenesis. Interestingly, OXPHOS signature was inversely correlated with His level in SLE B cells.

Conclusion:

His may be an important factor for SLE pathogenesis especially in B cells independently from IFN signal. SLC15A4, a transporter of His on lysosome, is one of the SLE GWAS SNPs and has been reported to play an important role in IFN production in B cells through regulation of TLR7/9 activation 2). We also identified that SLE patients with risk allele of SLC15A4 had tendency to show higher plasma His level, indicating His homeostasis could become a novel treatment target for SLE. Moreover, the inverse correlation of His level to SDI as well as OXPHOS signature suggests that His might play a key role for promoting organ damages in SLE.

References:

[1]Nat Genet.2017;49:568. 2)Immunity. 2014;41:375. 3)Semin Arthritis Rheum.2019;48:1142

Disclosure of Interests: :

Yukiko Iwasaki: None declared, Yusuke Takeshima: None declared, Masahiro Nakano: None declared, Mineto Ota: None declared, Yasuo Nagafuchi: None declared, Akari Suzuki: None declared, Yuta Kochi: None declared, Tomohisa Okamura: None declared, Takaho Endo: None declared, Ichiro Miki: None declared, Kazuhiro Sakurada: None declared, Kazuhiko Yamamoto Grant/research support from: Astellas, BMS, MitsubishiTanabe, Pfizer, Ayumi, Takeda, Chugai, Eisai, Taisho Toyama, UCB, and ImmunoFuture, Keishi Fujio Grant/research support from: Astellas, BMS, MitsubishiTanabe, Pfizer, Ayumi, Takeda, Chugai, Eisai, Taisho Toyama, Eli Lilly, Sanofi, and UCB

Differences in fetal fractional limb volume changes in normal and gestational diabetic pregnancies: an exploratory observational study

OBJECTIVE

Fetal fractional limb volume has been proposed as a useful measure for quantifying fetal soft tissue development. The aim of this study was to investigate the growth of fractional arm volume (AVol) and fractional thigh volume (TVol) of fetuses with maternal gestational diabetes (GDM) compared with those of fetuses with normal glucose tolerance (NGT). We hypothesised fetal fractional limb volume would be larger in the GDM group than in the NGT group in late gestation.

DESIGN

Exploratory observational study.

SETTING

Saitama Municipal Hospital.

SAMPLE

A total of 165 (125 NGT and 40 GDM) singleton Japanese pregnant women.

METHODS

AVol and TVol were assessed between 20 and 37 weeks' gestation as cylindrical limb volumes based on 50% of the fetal humeral or femoral diaphysis length. Women were diagnosed as GDM based on the criteria of the Japan Society of Obstetrics and Gynecology.

MAIN OUTCOME MEASURES

AVol and TVol were compared between women with NGT and those with GDM at each gestational age period (2-week intervals from 20 to 37 weeks' gestation).

RESULTS

Overall, 287 ultrasound scans were performed (NGT group, 205 scans; GDM group, 82 scans). There was no significant difference of AVol between the groups before 32 weeks' gestation. AVol was significantly larger in the GDM group than in the NGT group after 32 weeks' gestation (P < 0.05). TVol was not statistically different between the groups across gestation.

CONCLUSIONS

Detection of variations in fetal AVol may provide greater insight into understanding the origins of altered fetal body proportion in GDM.

TWEETABLE ABSTRACT

AVol, but not TVol, is significantly larger in fetuses with GDM than in those with NGT after 32 weeks' gestation.

Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA

Background

Upstream open reading frames (uORFs) in the 5′-untranslated regions (5′-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that control translation of downstream main ORFs (mORFs). For genome-wide searches for uORFs with conserved peptide sequences (CPuORFs), comparative genomic studies have been conducted, in which uORF sequences were compared between selected species. To increase chances of identifying CPuORFs, we previously developed an approach in which uORF sequences were compared using BLAST between Arabidopsis and any other plant species with available transcript sequence databases. If this approach is applied to multiple plant species belonging to phylogenetically distant clades, it is expected to further comprehensively identify CPuORFs conserved in various plant lineages, including those conserved among relatively small taxonomic groups.

Results

To efficiently compare uORF sequences among many species and efficiently identify CPuORFs conserved in various taxonomic lineages, we developed a novel pipeline, ESUCA. We applied ESUCA to the genomes of five angiosperm species, which belong to phylogenetically distant clades, and selected CPuORFs conserved among at least three different orders. Through these analyses, we identified 89 novel CPuORF families. As expected, ESUCA analysis of each of the five angiosperm genomes identified many CPuORFs that were not identified from ESUCA analyses of the other four species. However, unexpectedly, these CPuORFs include those conserved across wide taxonomic ranges, indicating that the approach used here is useful not only for comprehensive identification of narrowly conserved CPuORFs but also for that of widely conserved CPuORFs. Examination of the effects of 11 selected CPuORFs on mORF translation revealed that CPuORFs conserved only in relatively narrow taxonomic ranges can have sequence-dependent regulatory effects, suggesting that most of the identified CPuORFs are conserved because of functional constraints of their encoded peptides.

Conclusions

This study demonstrates that ESUCA is capable of efficiently identifying CPuORFs likely to be conserved because of the functional importance of their encoded peptides. Furthermore, our data show that the approach in which uORF sequences from multiple species are compared with those of many other species, using ESUCA, is highly effective in comprehensively identifying CPuORFs conserved in various taxonomic ranges.

P856Incidence and Outcomes of irregular protrusion after stent implantation in patients with acute myocardial infarction: An in in vivo optical coherence tomography study

Background

Irregular protrusion, a protrusion of material with an irregular surface into the lumen of the vessel after stent implantation, can only be identified by optical coherence tomography (OCT). A previous study demonstrated that irregular protrusion after stent implantation was an independent predictor of 1-year major adverse cardiac events (MACE) in CAD patients. However, the true incidence and prognostic significance of irregular protrusion after stenting in patients with ST-segment elevation myocardial infarction (STEMI) have not previously examined.

Aims

The aims of this study were the following: 1) to evaluate the incidence of irregular protrusion detected by OCT in STEMI patients after stenting; and 2) to compare the long-term outcomes between patients with and without irregular protrusion.

Methods and results

A total of 210 STEMI patients who had post-procedure OCT imaging after coronary stenting within 12 hours after symptom onset were studied. We divided them into two groups: those with irregular protrusion (n=159) and those without (n=51) after stenting. There were no significant differences in baseline characteristics between the 2 groups except that peak CK-MB levels were higher in patients with irregular protrusion than those without (289 (137–563) vs. 260 (63–349) U/L, p<0.05). During mean follow-up period of 298 days, the overall incidence of MACE defined as cardiac death, target vessel-related myocardial infarction, and target lesion revascularization was 15.3%. Kaplan-Meier curve showed that the incidence of MACE did not differ between patients with and without irregular protrusion (14.7% vs. 17.7%, p=0.53 by Log-rank).

Conclusions

Irregular protrusion after stent implantation was detected in three-fourth of STEMI patients. Although patients with irregular protrusion had a greater myocardial damage, it did not influence clinical outcomes.

Acknowledgement/Funding

Donation course from Abbott Japan

P2810Clinical outcomes 1 year after filter protection during percutaneous coronary intervention in patients with attenuated plaque identified by intravascular ultrasound

Background

In the VAMPIRE 3 (VAcuuM asPIration thrombus REemoval 3) trial, we have previously shown that selective use of distal filter protection during percutaneous coronary intervention (PCI) decreased the incidence of no-reflow phenomenon and was associated with fewer in-hospital serious adverse cardiac events than conventional PCI in patients with attenuated plaque ≥5mm. However, whether the early efficacy of distal embolic protection translate into long term clinical benefit is unknown.

Methods

Patients with acute coronary syndrome (ACS) with attenuated plaque ≥5mm were assigned to distal protection (DP) (n=98) or conventional treatment (CT) (n=96). The primary end point of the incidence of no-reflow phenomenon during PCI and the secondary end point of in-hospital serious adverse cardiac events has been reported previously. The rate of a major adverse events, a composite of death from any cause, non-fatal myocardial infarction, or unplanned target vessel revascularization (TVR) at 1 year was the prespecified secondary end point of the trial. All clinical endpoint events were adjudicated by an independent Clinical Event Committee.

Results

Major adverse events at 1 year occurred in 12 patients (12.2%) in the DP group and in 3 patients (3.1%) in the CT group (P=0.029). The difference was driven by a higher risk of TVR (11 [11.2%] vs. 2 [2.1%], p=0.018) in the DP group compared with the CT group. In patients treated with bare metal stents (n=42), major adverse events occurred in 25.0% of the patients in the DP group and in none of the patients in the CT group (P=0.029), whereas in patients treated with drug eluting stents (n=152), rates of major adverse events were similar between the groups (8.1% vs. 3.9%, p=0.32). Rates of cardiac death were not significantly different (1.0% vs. 1.0%, p=1.00). No definite stent thrombosis was observed in either group.

Conclusions

In the VAMPIRE 3 trial of patients with ACS with attenuated plaque ≥5mm, the 1-year rates of major adverse events in the distal protection group were higher than in the conventional treatment group. This effect could be mitigated by the use of drug eluting stents.

Acknowledgement/Funding

This work was supported in part by a grant from Nipro, Boston Scientific Corporation, and Japan Lifeline.

Computational Drug-repositioning Approach Identifying Sirolimus as a Potential Therapeutic Option for Inflammatory Dilated Cardiomyopathy

OBJECTIVE

The aim of this study was to determine promising treatment options for human inflammatory dilated cardiomyopathy using a computational drug-repositioning approach (repurposing established drug compounds for new therapeutic indications).

BACKGROUND

If the myocardial tissue is detected to be infiltrated with inflammatory cells, primarily of lymphocytes, and if the virus is confirmed using genetic examination (PCR) or immunostaining, the infection is suspected. However, there is no specific treatment (i. e., an antiviral drug) even if the virus is identified; therefore, we used Connectivity Map to identify compounds showing inverse drug-disease signatures, indicating activity against inflammatory dilated cardiomyopathy.

RESULTS

Potential drug-repositioning candidates for the treatment of inflammatory dilated cardiomyopathy were explored through a systematic comparison of the gene expression profiles induced by drugs using Gene Expression Omnibus and Connectivity Map databases.

CONCLUSION

Using a computational drug-repositioning approach based on the integration of publicly available gene expression signatures of drugs and diseases, sirolimus was suggested as a novel therapeutic option for inflammatory dilated cardiomyopathy.

Prognostic nutritional index and early mortality with percutaneous endoscopic gastrostomy

BACKGROUND

Although percutaneous endoscopic gastrostomy (PEG) is a well-accepted and less invasive method of feeding tube placement in patients with swallowing difficulties, complications and early death after PEG have been reported.

AIM

This study aimed to evaluate predictive factors associated with 30-day mortality after PEG, and to assess the utility of nutritional supporting period before PEG in reducing early mortality following PEG.

DESIGN

An observational study.

METHODS

We retrospectively analyzed 268 patients who underwent PEG at Sapporo Shirakaba-dai Hospital from 2006 to 2010, using clinical and laboratory data to analyze predictive factors associated with early death after PEG. Then, we prospectively assessed 152 consecutive patients assessed for eligibility for PEG from 2011 to 2014. We assessed the patients' nutritional condition using Onodera's prognostic nutritional index (PNI), and supported nutrition for more than 10 days before PEG in patients with a poor nutritional index (PNI < 37).

RESULTS

In both univariate and multivariate analyses in the retrospective study, Onodera's PNI of less than 37 was the only predictive factor for early mortality. In the second study, among the 115 patients who finally underwent PEG, early mortality rates improved to 1.7% from 5.2% in the first study. Conversely, 32% of patients with malnutrition who did not undergo PEG died within 30 days.

CONCLUSION

Nutritional status might be a predictive factor for early mortality after PEG. In patients with poor nutritional status, nutritional supporting period before PEG might improve the outcomes and reduce unnecessary PEG.

Comprehensive phylogenomic analysis reveals a novel cluster of simian endogenous retroviral sequences in Colobinae monkeys

Simian retrovirus (SRV) is a type-D betaretrovirus infectious to the Old World monkeys causing a variety of symptoms. SRVs are also present in the Old World monkey genomes as endogenous forms, which are referred to as Simian endogenous retroviruses (SERVs). Although many SERV sequences have been identified in Cercopithecinae genomes, with potential of encoding all functional genes, the distribution of SERVs in genomes and evolutionary relationship between exogeneous SRVs and SERVs remains unclear. In this study, we comprehensively investigated seven draft genome sequences of the Old World monkeys, and identified a novel cluster of SERVs in the two Rhinopithecus (R. roxellana and R. bieti) genomes, which belong to the Colobinae subfamily. The Rhinopithecus genomes harbored higher copy numbers of SERVs than the Cercopithecinae genomes. A reconstructed phylogenetic tree showed that the Colobinae SERVs formed a distinct cluster from SRVs and Cercopithecinae SERVs, and more closely related to exogenous SRVs than Cercopithecinae SERVs. Three radical amino acid substitutions specific to Cercopithecinae SERVs, which potentially affect the infectious ability of SERVs, were also identified in the proviral envelope protein. In addition, we found many integration events of SERVs were genus- or species-specific, suggesting the recent activity of SERVs in the Old World monkey genomes. The results suggest that SERVs in Cercopithecinae and Colobinae monkeys were endogenized after the divergence of subfamilies and do not transmit across subfamilies. Our findings also support the hypothesis that Colobinae SERVs are direct ancestors of SRV-6, which has a different origin from the other exogenous SRVs. These findings shed novel insight into the evolutionary history of SERVs, and may help to understand the process of endogenization of SRVs.

In Vitro and in Vivo Antigen-Induced Release of High-Molecular Weight Neutrophil Chemotactic Activity from Human Nasal Tissue

High molecular weight neutrophil chemotactic activity has been identified in resected human nasal polyps, inferior turbinates, and nasal secretions following antigen challenge. The estimated molecular weight, by gel filtration chromatography, was approximately 600,000. However, a heterogeneity of molecular weight in some patients was recognized. Our results suggest a possible role for high molecular weight-neutrophil chemotactic activity in the pathogenesis of hypersensitivity in the human nasal cavity.

Abstract P4-01-10: Development of photoacoustic vascular imaging system for breast cancer

Background:

Tumor angiogenesis and hypoxia are associated with breast cancer growth and metastasis. Photoacoustic (PA) tomography is an optical imaging technology that visualizes distribution and oxygenation status of hemoglobin with high spatial resolution. Initially we developed a photoacoustic mammography (PAM) having a flat-shaped scanning detector that could detect breast tumors. Nevertheless, the flat-shaped detector array has the drawback of a limited view. Here we developed a novel PAM system with a hemispherical-shaped detector array (HDA), which enables us to identify microvasculatures non-invasively and allow the collection of nearly spatially isotropic three-dimensional reconstructed image of blood vessels. This non-invasive vascular imaging system may be able to characterize tumor angiogenesis and analyze the status of microcirculation. The aim of this study was to analyze the imaging findings of tumor-related vasculature in breast cancer patients.

Patients and method:

A PAM system with HDA has been generated in a cooperation project between Canon Inc., Japan, and Kyoto University. Twenty-two primary breast cancer patients, including 5 patients with non-invasive cancer and 17 patients with invasive cancer, diagnosed between December 2014 and December 2015 underwent the PAM imaging analysis. We also applied the breast deformation algorithm from the breast shape in a MRI image to that in a PA image in order to create a fusion image of the two modalities for the analysis. Features of peri- and intra-tumoral vasculature, and their oxygenation status were evaluated. The study protocol was approved by the institutional review board at Kyoto University Hospital (UMIN000012251). All patients provided informed consent to participate in this study.

Results:

The abnormal peri-tumoral vasculature was detected in 86% of all non-invasive and invasive disease cases. In invasive cancer cases, most tumor-related blood vessels were centripetally directed toward the tumor, and 93% of centripetal blood vessels appeared to be disrupted or rapidly narrowed at the tumor boundary. The centripetal blood vessel structure was frequently observed in invasive cancer compared with non-invasive cancer (61% vs 35%). PA images before and after preoperative chemotherapy were obtained in one case, where intra-tumoral blood vessels became finer after chemotherapy, reflecting normalization of intra-tumoral microcirculation induced by chemotherapy.

Conclusions:

A PAM system with HDA has provided a high-resolution vascular images of primary breast cancers. The morphological differences of peri-tumoral vasculature were observed between invasive disease and non-invasive disease. These results suggest the potential of PA imaging as a non-invasive tool to analyze tumor vasculature of human breast cancers and maybe be helpful for breast cancer diagnosis.

(Acknowledgements)

This work was partially supported by the Innovative Techno-Hub for Integrated Medical Bio-imaging Project of the Special Coordination Funds for Promoting Science and Technology from the Ministry of Education, Culture, Sports, Science, and Technology, Japan.

Citation Format: Toi M, Asao Y, Takada M, Kataoka M, Endo T, Kawashima M, Yamaga I, Nakayama Y, Tokiwa M, Fakhrejahani E, Torii M, Kawaguchi-Sakita N, Kanao S, Matsumoto Y, Yagi T, Sakurai T, Togashi K, Shiina T. Development of photoacoustic vascular imaging system for breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-01-10.

Visualization of tumor-related blood vessels in human breast by photoacoustic imaging system with a hemispherical detector array

Noninvasive measurement of the distribution and oxygenation state of hemoglobin (Hb) inside the tissue is strongly required to analyze the tumor-associated vasculatures. We developed a photoacoustic imaging (PAI) system with a hemispherical-shaped detector array (HDA). Here, we show that PAI system with HDA revealed finer vasculature, more detailed blood-vessel branching structures, and more detailed morphological vessel characteristics compared with MRI by the use of breast shape deformation of MRI to PAI and their fused image. Morphologically abnormal peritumoral blood vessel features, including centripetal photoacoustic signals and disruption or narrowing of vessel signals, were observed and intratumoral signals were detected by PAI in breast cancer tissues as a result of the clinical study of 22 malignant cases. Interestingly, it was also possible to analyze anticancer treatment-driven changes in vascular morphological features and function, such as improvement of intratumoral blood perfusion and relevant changes in intravascular hemoglobin saturation of oxygen. This clinical study indicated that PAI appears to be a promising tool for noninvasive analysis of human blood vessels and may contribute to improve cancer diagnosis.

Nutritional assessment using stable isotope ratios of carbon and nitrogen in the scalp hair of geriatric patients who received enteral and parenteral nutrition formulas

BACKGROUND & AIMS

The δ¹³C and δ¹⁵N values in the scalp hair of geriatric patients in Japan who received the enteral or parenteral nutrition formula were measured to assess nutritional status.

METHODS

The relations among δ¹³C, δ¹⁵N, calorie intake, BMI, albumin concentration, total cholesterol (T-CHO) and geriatric nutritional risk index (GNRI) in the patients were investigated. Furthermore, the enrichment of δ¹³C and δ¹⁵N from the nutrients to the hair was investigated.

RESULTS

The δ¹³C values in the hair of patients who received enteral nutrition decreased with decreases in the calories received, while the δ¹⁵N values increased, suggesting malnutrition in some patients with a low calorie intake due to a negative nitrogen balance. The distribution of patients with a low calorie intake (below 20 kcal/kg/day) when δ¹³C was plotted against δ¹⁵N differed from that of control subjects, but the distribution of patients with a high calorie intake (above 20 kcal/kg/day) was similar to that of control subjects. No significant differences were observed in BMI, albumin concentration, T-CHO or GNRI between the low and high calorie groups. The enrichment of δ¹³C and δ¹⁵N from the enteral nutrients to the hair were inversely correlated with the δ¹³C and δ¹⁵N in the enteral nutrients. The enrichment levels of δ¹³C and δ¹⁵N tended to be higher and lower, respectively, in the high calorie group. On the other hand, the δ¹³C and δ¹⁵N values in the hair of patients who received parenteral nutrition were higher and lower than those in the control subjects and in the patients who received enteral nutrition, respectively, reflecting the higher δ¹³C and lower δ¹⁵N contents of the parenteral nutrients.

CONCLUSIONS

The δ¹³C and δ¹⁵N values in the hair of patients who received enteral nutrition may be effective indicators for evaluating the long-term nutritional status of geriatric patients. A calorie intake of 20 kcal/kg/day may be a cut-off value for malnutrition in Japanese geriatric patients receiving enteral nutrition. However, caution is necessary when dealing with patients switching from parental nutrition as parenteral nutrition resulted in different changes in δ¹³C and δ¹⁵N. The enrichment levels of δ¹³C and δ¹⁵N from the enteral nutrients to the hair may be inversely correlated with the δ¹³C and δ¹⁵N values of enteral nutrients and vary according to the calorie intake.

Development of a cascade arc discharge source for an atmosphere-vacuum interface device

To realize a novel vacuum-atmosphere interface that does not require a large differential pumping system, a robust cascade arc discharge source called a plasma window is constructed and tested for long-term operation. By modifying a test plasma with a direct current discharge, a vacuum interface with a high gas pressure ratio of 1/407 between the discharge and expansion sections is demonstrated for currents as high as 20 A. No significant damage to the electrodes is observed during the operation. Analysis of the visible emission spectra reveals that a stationary, stable argon plasma having a temperature of 1 eV and a density of 1.5 × 10(16) cm(-3) is generated in the plasma channel.

MR Imaging of Hippocampal Sulcus Remnant: Age-Related Differences

The hippocampal sulcus remnant (HSR) is often observed at the medial temporal lobe on MR images. In the present study, we made a retrospective assessment of the frequency and age-related differences in HSR in routine brain MR examinations of 1000 patients, 494 females and 506 males. Cases with one or several spots that were hypointense on T1-weighted and FLAIR images and hyperintense on T2-weighted images were defined as positive for HSR. Abnormal spots with the same intensity as cerebrospinal fluid were observed in 210 out of 506 males and in 193 out of 494 females. No significant sex-related differences were observed in the frequency of HSR. The HSR was seen more frequently with age in both males and females. Patients with hypertension had a significantly higher frequency of HSR.

Measurement and comparison of individual external doses of high-school students living in Japan, France, Poland and Belarus-the 'D-shuttle' project

Twelve high schools in Japan (of which six are in Fukushima Prefecture), four in France, eight in Poland and two in Belarus cooperated in the measurement and comparison of individual external doses in 2014. In total 216 high-school students and teachers participated in the study. Each participant wore an electronic personal dosimeter 'D-shuttle' for two weeks, and kept a journal of his/her whereabouts and activities. The distributions of annual external doses estimated for each region overlap with each other, demonstrating that the personal external individual doses in locations where residence is currently allowed in Fukushima Prefecture and in Belarus are well within the range of estimated annual doses due to the terrestrial background radiation level of other regions/countries.

An automated method for detecting architectural distortions on mammograms using direction analysis of linear structures

Architectural distortion is one of the most important findings when evaluating mammograms for breast cancer. Abnormal breast architecture is characterized by the presence of spicules, which are distorted mammary structures that are not accompanied by an increased density or mass. We have been developing an automated method for detecting spiculated architectural distortions by analyzing linear structures extracted by normal curvature. However, some structures that are possibly related to distorted areas are not extracted using this method. The purpose of this study was to develop a new automated method for direction analysis of linear structures to improve detection performance in mammography. The direction of linear structures in each region of interest (ROI) was first determined using a direction filter and a background filter that can define one of eight directions (0°, 22.5°, 45°, 67.5°, 90°, 112.5°, 135°, and 157.5°). The concentration and isotropic indexes were calculated using the determined direction of the linear structures in order to extract the candidate areas. Discriminant analysis was performed to eliminate false positives results. Our database consisted of 168 abnormal images containing 174 distorted areas and 580 normal images. The sensitivity of the new method was 81%. There were 2.6 and 4.2 false positives per image using the new and previous methods, respectively. These findings show that our new method is effective for detecting spiculated architectural distortions.

Occurrence of adverse events caused by valganciclovir as pre-emptive therapy for cytomegalovirus infection after allogeneic stem cell transplantation is reduced by low-dose administration

BACKGROUND

Pre-emptive therapy with valganciclovir (VGCV) has become the standard therapy for preventing cytomegalovirus (CMV) infection after allogeneic hematopoietic stem cell transplantation (HSCT). The effectiveness of low-dose VGCV (900 mg per day) has been shown to be equal to that of standard-dose VGCV (900 mg twice daily); however, individualized optimal dosing and toxicity of VGCV have not been reported.

METHODS

We conducted a retrospective study to evaluate the optimal dose of VGCV as pre-emptive therapy for preventing CMV infection by comparing the frequency of adverse events (AEs) and clinical efficacy in a low-dose VGCV group with those in a standard-dose VGCV group. Thirty-eight patients who were administered VGCV because of CMV antigenemia after HSCT were analyzed.

RESULTS

Neutropenia (standard-dose group: 33%, low-dose group: 15%, P = 0.26) and thrombocytopenia (standard-dose group: 39%, low-dose group: 15%, P = 0.14) were frequent AEs of VGCV, and a significantly higher frequency of overall AEs was detected in the standard-dose group than in the low-dose group (P < 0.01). In comparison of dosage based on weight, dosage of VGCV >27 mg/kg was closely related to onset of AEs (P = 0.04).

CONCLUSIONS

Low-dose VGCV was not inferior in clinical efficacy, including clearance rate of CMV antigenemia and incidence of consequent CMV disease, to standard-dose VGCV as was previously reported. Initial low-dose VGCV for pre-emptive CMV therapy markedly reduces hematologic toxicity and has clinical efficacy equivalent to that of standard-dose VGCV. It is therefore reasonable for patients, except for noticeably overweight patients, to be given initial low-dose VGCV.

Cysteine amide adduct formation from carboxylic acid drugs via UGT-mediated bioactivation in human liver microsomes

Although chemical trapping has been widely used to evaluate cytochrome P450-mediated drug bioactivation, thus far, only a few in vitro-trapping studies have been performed on UDP-glucuronosyltransferase (UGT)-mediated drug bioactivation. In this study, we used cysteine (Cys) as trapping agent to gain new insights into the UGT-mediated bioactivation involving acyl glucuronides of carboxylic acid drugs. Diclofenac, ketoprofen and ibuprofen were incubated in human liver microsomes with UDPGA and Cys, followed by analysis using ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS). The N-acyl-Cys amide adduct of diclofenac was characterized by mass analysis and was detectable even in photodiode array analysis. Our data indicated that the formation of such adducts reflects the reactivity of the corresponding acyl glucuronides. In addition, it was suggested that the adduct formation requires an N-terminal Cys moiety with both a free amine and a free thiol group, from the results using various cysteine derivatives. We propose that the S-acyl-Cys thioester adduct can form via transacylation of an acyl glucuronide and can then form to an N-acyl-Cys amide adduct through intramolecular S- to N-acyl rearrangement. This series of the reactions has important implications as a possible bioactivation mechanism for covalent binding of carboxylic acid drugs to macromolecules.