Dual-wield NTPases: A novel protein family mined from AlphaFold DB

AlphaFold protein structure database (AlphaFold DB) archives a vast number of predicted models. We conducted systematic data mining against AlphaFold DB and discovered an uncharacterized P-loop NTPase family. The structure of the protein family was surprisingly novel, showing an atypical topology for P-loop NTPases, noticeable twofold symmetry, and two pairs of independent putative active sites. Our findings show that structural data mining is a powerful approach to identifying undiscovered protein families.

Elastic network model reveals distinct flexibilities of capping proteins bound to CARMIL and twinfilin-tail

Capping protein (CP) binds to the barbed end of an actin-filament and inhibits its elongation. CARMIL binds CP and dissociates it from the barbed end of the actin-filament. The binding of CARMIL peptide alters the flexibility of CP, which is considered to facilitate the dissociation. Twinfilin also binds to CP through its C-terminal tail. The complex structures of the CP/twinfilin-tail (TW-tail) peptide indicate that the binding sites of CARMIL and TW-tail overlap. However, TW-tail binding does not facilitate the dissociation of CP from the barbed end. We extensively investigated the flexibilities of CP in the CP/TW-tail or CP/CARMIL complexes using an elastic network model and concluded that TW-tail binding does not alter the flexibility of CP. Our extensive analysis also highlighted that the strong contacts of peptides with the two domains of CP, that is, the CP-L and CP-S domains, are key to changing the flexibilities of CP. CARMIL peptides can interact strongly with both of the domains, while TW-tail peptides exclusively interact with the CP-S domain because the binding site of TW-tail on CP relatively shifts to the CP-S domain compared with that of CP/CARMIL. This result supports our hypothesis that the dissociation of CP from the barbed end is regulated by the flexibility of CP.

Prediction of chaperonin GroE substrates using small structural patterns of proteins

Molecular chaperones are indispensable proteins that assist the folding of aggregation-prone proteins into their functional native states, thereby maintaining organized cellular systems. Two of the best-characterized chaperones are the Escherichia coli chaperonins GroEL and GroES (GroE), for which in vivo obligate substrates have been identified by proteome-wide experiments. These substrates comprise various proteins but exhibit remarkable structural features. They include a number of α/β proteins, particularly those adopting the TIM β/α barrel fold. This observation led us to speculate that GroE obligate substrates share a structural motif. Based on this hypothesis, we exhaustively compared substrate structures with the MICAN alignment tool, which detects common structural patterns while ignoring the connectivity or orientation of secondary structural elements. We selected four (or five) substructures with hydrophobic indices that were mostly included in substrates and excluded in others, and developed a GroE obligate substrate discriminator. The substructures are structurally similar and superimposable on the 2-layer 2α4β sandwich, the most popular protein substructure, implying that targeting this structural pattern is a useful strategy for GroE to assist numerous proteins. Seventeen false positives predicted by our methods were experimentally examined using GroE-depleted cells, and 9 proteins were confirmed to be novel GroE obligate substrates. Together, these results demonstrate the utility of our common substructure hypothesis and prediction method.

How AlphaFold2 Predicts Conditionally Folding Regions Annotated in an Intrinsically Disordered Protein Database, IDEAL

AlphaFold2 (AF2) is a protein structure prediction program which provides accurate models. In addition to predicting structural domains, AF2 assigns intrinsically disordered regions (IDRs) by identifying regions with low prediction reliability (pLDDT). Some regions in IDRs undergo disorder-to-order transition upon binding the interaction partner. Here we assessed model structures of AF2 based on the annotations in IDEAL, in which segments with disorder-to-order transition have been collected as Protean Segments (ProSs). We non-redundantly selected ProSs from IDEAL and classified them based on the root mean square deviation to the corresponding region of AF2 models. Statistical analysis identified 11 structural and sequential features, possibly contributing toward the prediction of ProS structures. These features were categorized into two groups: one that contained pLDDT and the other that contained normalized radius of gyration. The typical ProS structures in the former group comprise a long α helix or a whole or part of the structural domain and those in the latter group comprise a short α helix with terminal loops.

Computational Methods to Predict Intrinsically Disordered Regions and Functional Regions in Them

Intrinsically disordered regions (IDRs) are protein regions that do not adopt fixed tertiary structures. Since these regions lack ordered three-dimensional structures, they should be excluded from the target portions of homology modeling. IDRs can be predicted from the amino acid sequences, because their amino acid compositions are different from that of the structured domains. This chapter provides a review of the prediction methods of IDRs and a case study of IDR prediction.

Classification of proteins inducing liquid-liquid phase separation: sequential, structural and functional characterization

Liquid-liquid phase separation (LLPS) within the cell can form biological condensates, which are increasingly recognized to play important roles in various biological processes. Most proteins involved in LLPS are known to be intrinsically disordered proteins containing intrinsically disordered regions (IDRs) with low complexity regions (LCRs). The proteins driving LLPS were selected from databases of LLPS-related proteins and then classified into three classes according to the components in the condensates. Through in silico analyses, we found that proteins in the homo class, those that induce LLPS without partner molecules, have different IDRs and LCRs compared with the reference proteome. In contrast, proteins in the other classes, those that induce LLPS with partner proteins (the hetero class) or nucleic acids (the mixed class), did not show a clear difference to the reference proteome in IDRs and LCRs. The hetero-class proteins contained structural domains to serve protein-protein interactions, and the mixed-class ones had the structural domains associated with nucleic acids. These results suggest that IDRs in the homo-class proteins have unique IDRs, which provide multivalent interaction sites required for LLPS, whereas the hetero- and mixed-class proteins can induce LLPS through the combination of the interaction among LCRs, structural domains, and nucleic acids.

Causes of pre-treatment loss to follow-up in patients with TB

SETTING

Five urban TB diagnostic centres in Lusaka, Zambia.

OBJECTIVE

To determine the proportion of bacteriologically confirmed pre-treatment lost to follow-up (LTFU) patients with TB found at the study settings in 2020.

DESIGN

This was a retrospective cohort study in which the TB laboratory and treatment registers at the study sites were cross-matched.

RESULTS

A total of 1,085 bacteriologically confirmed patients with TB were found in the laboratory TB registers at the study settings. Of these, 809 (74.6%) were males, whereas 8 (0.7%) were children, 1,005 (92.6%) were diagnosed using Xpert, 78 (7.2%) by microscopy. A total of 91 (8.4%, 95% CI 6.8-10.2) were determined to be pre-treatment LTFU. Those who had very low (14.0%, 95% CI 8.5-21.2) and low (11.8%, 95% CI 8.4-16.0) results on Xpert were respectively 3.1 (95% CI 1.6-6.0) and 2.6 (95% CI 1.4-4.8) times more likely to become pre-treatment LTFU than those who had medium (4.5%, 95% CI 2.5-7.4) results. The proportions of pre-treatment LTFU varied among the study sites from 0.7% to 16.1%.

CONCLUSION

Health facilities should strive to account for every patient with TB, with particular attention to those who are bacteriologically confirmed.

TB-related technical enquiries received in Japan, 2017-2019

SETTING

Japan, an intermediate TB burden country.

OBJECTIVE

To review TB-related technical enquiries received at the Research Institute of Tuberculosis, Japan, from January 2017 to December 2019.

DESIGN

This was a cohort study.

RESULTS

A total of 2,197 enquiries were analysed. On average, 61.0 enquiries/month (range: 42-81) were received. The enquiry rates were highest for the Yamanashi (4.65/100,000 population) and Ishikawa (4.55) Prefectures, and lowest in the Yamagata (0.46) and Tochigi (0.56) Prefectures. The main organisations the enquirers belonged to were local governments (n = 1,585, 72.1%) and healthcare facilities (n = 307, 14.0%). The enquirers were medical doctors (n = 391, 17.8%), nurses (n = 1,207, 54.9%), other healthcare professionals (n = 57, 2.6%), the general public (n = 168, 7.6%) and others/unknown (n = 374, 17.0%). The most frequent enquiries were about TB diagnosis and treatment (n = 501, 22.8%), including laboratory diagnosis (n = 88, 4.0%), TB treatment in general (n = 93, 4.2%) and management of comorbidities (n = 86, 3.9%), followed by contact investigations (n = 385, 17.5%) and TB in foreigners (n = 344, 15.7%).

CONCLUSION

As the most frequent enquiries were about diagnosis and treatment of TB, the health ministry of Japan should maintain a few specialised TB institutions with TB physicians to provide technical assistance.

High-power laser experiment on developing supercritical shock propagating in homogeneously magnetized plasma of ambient gas origin

A developing supercritical collisionless shock propagating in a homogeneously magnetized plasma of ambient gas origin having higher uniformity than the previous experiments is formed by using high-power laser experiment. The ambient plasma is not contaminated by the plasma produced in the early time after the laser shot. While the observed developing shock does not have stationary downstream structure, it possesses some characteristics of a magnetized supercritical shock, which are supported by a one-dimensional full particle-in-cell simulation taking the effect of finite time of laser-target interaction into account.

Direct observations of pure electron outflow in magnetic reconnection

Magnetic reconnection is a universal process in space, astrophysical, and laboratory plasmas. It alters magnetic field topology and results in energy release to the plasma. Here we report the experimental results of a pure electron outflow in magnetic reconnection, which is not accompanied with ion flows. By controlling an applied magnetic field in a laser produced plasma, we have constructed an experiment that magnetizes the electrons but not the ions. This allows us to isolate the electron dynamics from the ions. Collective Thomson scattering measurements reveal the electron Alfvénic outflow without ion outflow. The resultant plasmoid and whistler waves are observed with the magnetic induction probe measurements. We observe the unique features of electron-scale magnetic reconnection simultaneously in laser produced plasmas, including global structures, local plasma parameters, magnetic field, and waves.

OP0110 CELL-TYPE-SPECIFIC TRANSCRIPTOME ARCHITECTURE UNDERLYING THE ESTABLISHMENT AND EXACERBATION OF SYSTEMIC LUPUS ERYTHEMATOSUS

Background

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with unknown etiology involving multiple immune cells and has diverse clinical phenotypes. This heterogeneous nature has hampered a better understanding of SLE pathogenesis and the development of effective therapeutic agents. While recent single-cell RNA sequencing studies of SLE identified several important cell subpopulations, they were limited by sparse expression information at single-cell level and small sample sizes.

Objectives

This study aimed to elucidate the dysregulated gene expression pattern linked to multiple clinical statuses of SLE with a fine cellular resolution and higher sensitivity. We also attempted to resolve a complex interaction between risk variants and the transcriptome dysregulation seen in SLE patients.

Methods

We conducted a large-scale bulk transcriptome study of 6,386 RNA-sequencing data including 27 purified immune cell types in peripheral blood from 136 SLE and 89 healthy donors in the Immune Cell Gene Expression Atlas from the University of Tokyo (ImmuNexUT) cohort1. At enrollment, SLE patients had diverse clinical manifestations (disease activity, organ involvement and treatment profiles) and 22 patients were re-evaluated after belimumab treatment.

Results

We first profiled two distinct cell-type-specific transcriptomic signatures: disease-state and disease-activity signatures, reflecting disease establishment and exacerbation, respectively.

After confirming the high replicability of both signatures in independent cohorts, we identified candidates of biological processes unique to each signature: e.g., upregulated E2F transcriptional activity in Th1, CD8+ memory T-lineage and NK cells, and dynamic increase of IL21 and CXCL13 in Th1 cells in an active phase of SLE. Pathway analysis highlighted the importance of immunometabolic process for SLE (e.g., oxidative phosphorylation) in cell-type-specific resolution.

Moreover, we demonstrated cell-type-specific contributions to diverse organ involvement, e.g., Th1 for mucocutaneous, monocyte-lineage cells for musculoskeletal, neutrophil-lineage cells for renal activity, respectively.

We also observed the strong associations of disease-activity signatures with treatment effect: (i) belimumab suppressed activity signatures from B-lineage cells, especially in good responders and (ii) mycophenolate mofetil substantially suppressed activity signatures from plasmablast, Th1, and central memory CD8 cells.

However, through stratified LD score regression using large-scale SLE-GWASs, we revealed that disease-activity signatures were less enriched around SLE risk variants than disease-state signatures. Consistent with this result, the directions of SLE risk alleles’ expression quantitative trait locus (eQTL) effects were significantly concordant with the directions of disease-state signatures, but not with those of activity signatures. These findings suggested that the current genetic case-control studies may not well capture clinically vital biology linked to drug target discovery for SLE. Meanwhile, we also detected some examples of activity signatures that might contribute to the disease risk by modulating risk allele’s eQTL effects.

Figure 1.

Conclusion

We identified comprehensive gene signatures reflecting the establishment and exacerbation of SLE, which provide essential foundations for future genomic, genetic, and clinical studies.

References

[1]Ota, M. et al. Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases. Cell 2021;184:3006-21.e17.

Acknowledgements

This study was supported by Chugai Pharmaceutical Co., Ltd., Tokyo, Japan; the Ministry of Education, Culture, Sports; and the Japan Agency for Medical Research and Development (AMED) (JP21tm0424221 and JP21zf0127004).

Disclosure of Interests

Masahiro Nakano: None declared, Mineto Ota Grant/research support from: Mineto Ota belongs to the Social Cooperation Program, Department of functional genomics and immunological diseases, supported by Chugai Pharmaceutical., Yusuke Takeshima Grant/research support from: Yusuke Takeshima belonged to the Social Cooperation Program, Department of functional genomics and immunological diseases, supported by Chugai Pharmaceutical., Yukiko Iwasaki: None declared, Hiroaki Hatano: None declared, Yasuo Nagafuchi Grant/research support from: Yasuo Nagafuchi belongs to the Social Cooperation Program, Department of functional genomics and immunological diseases, supported by Chugai Pharmaceutical., Kwangwoo Kim: None declared, So-Young Bang: None declared, Hye Soon Lee: None declared, Hirofumi Shoda: None declared, Xuejun Zhang: None declared, Sang-Cheol Bae: None declared, Chikashi Terao: None declared, Kazuhiko Yamamoto: None declared, Tomohisa Okamura Grant/research support from: Tomohisa Okamura belongs to the Social Cooperation Program, Department of functional genomics and immunological diseases, supported by Chugai Pharmaceutical., Kazuyoshi Ishigaki: None declared, Keishi Fujio Speakers bureau: Keishi Fujio receives speaker fees from Chugai Pharmaceutical., Consultant of: Keishi Fujio receives consulting honoraria from Chugai Pharmaceutical., Grant/research support from: Keishi Fujio receives research support from Chugai Pharmaceutical.

High-power laser experiment forming a supercritical collisionless shock in a magnetized uniform plasma at rest

We present an experimental method to generate quasiperpendicular supercritical magnetized collisionless shocks. In our experiment, ambient nitrogen (N) plasma is at rest and well magnetized, and it has uniform mass density. The plasma is pushed by laser-driven ablation aluminum (Al) plasma. Streaked optical pyrometry and spatially resolved laser collective Thomson scattering clarify structures of plasma density and temperatures, which are compared with one-dimensional particle-in-cell simulations. It is indicated that just after the laser irradiation, the Al plasma is magnetized by a self-generated Biermann battery field, and the plasma slaps the incident N plasma. The compressed external field in the N plasma reflects N ions, leading to counterstreaming magnetized N flows. Namely, we identify the edge of the reflected N ions. Such interacting plasmas form a magnetized collisionless shock.

Evaluating cepharanthine analogues as natural drugs against SARS-CoV-2

Cepharanthine (CEP) is a natural biscoclaurine alkaloid of plant origin and was recently demonstrated to have anti‐severe acute respiratory syndrome coronavirus 2 (anti‐SARS‐CoV‐2) activity. In this study, we evaluated whether natural analogues of CEP may act as potential anti‐coronavirus disease 2019 drugs. A total of 24 compounds resembling CEP were extracted from the KNApSAcK database, and their binding affinities to target proteins, including the spike protein and main protease of SARS‐CoV‐2, NPC1 and TPC2 in humans, were predicted via molecular docking simulations. Selected analogues were further evaluated by a cell‐based SARS‐CoV‐2 infection assay. In addition, the efficacies of CEP and its analogue tetrandrine were assessed. A comparison of the docking conformations of these compounds suggested that the diphenyl ester moiety of the molecules was a putative pharmacophore of the CEP analogues.

Current status of structure-based drug repurposing against COVID-19 by targeting SARS-CoV-2 proteins

More than one and half years have passed, as of August 2021, since the COVID-19 caused by the novel coronavirus named SARS-CoV-2 emerged in 2019. While the recent success of vaccine developments likely reduces the severe cases, there is still a strong requirement of safety and effective therapeutic drugs for overcoming the unprecedented situation. Here we review the recent progress and the status of the drug discovery against COVID-19 with emphasizing a structure-based perspective. Structural data regarding the SARS-CoV-2 proteome has been rapidly accumulated in the Protein Data Bank, and up to 68% of the total amino acid residues encoded in the genome were covered by the structural data. Despite a global effort of in silico and in vitro screenings for drug repurposing, there is only a limited number of drugs had been successfully authorized by drug regulation organizations. Although many approved drugs and natural compounds, which exhibited antiviral activity in vitro, were considered potential drugs against COVID-19, a further multidisciplinary investigation is required for understanding the mechanisms underlying the antiviral effects of the drugs.

Analysis of 605 tuberculosis outbreaks in Japan, 1993-2015: time, place and transmission site

Since 1993, reports on tuberculosis (TB) outbreaks have been collected in Japan; however, there has never been an overall analysis of these TB outbreaks. We aim to provide one here. The TB outbreak data were obtained from the Ministry of Health, Labour and Welfare and are described in terms of time, place and transmission site. The average number of TB cases and latent tuberculosis infection (LTBI) were compared by the transmission site. Some 605 TB outbreaks with 3491 TB cases were reported in 1993-2015 with an increasing trend (r = 0.45), during which time 728 777 TB cases were reported nationwide. On an average, TB outbreaks occurred more often in April to May (5.5 outbreaks per 2 months) than in December to January (3.4). The most common transmission sites were workplaces (n = 255), followed by health facilities (n = 144), schools (n = 60) and welfare facilities (n = 48). Psychiatric hospitals and nursing homes had the highest average number of TB cases per outbreak (8.5 each), whereas schools and prisons had the highest numbers of LTBI cases (29.1 and 38.9, respectively). Countries, particularly those that have resources to investigate TB outbreaks, should collect and analyse findings of TB outbreaks, as it informs surveillance systems and eventually strengthens general health systems.

Re-evaluated treatment outcomes of bacteriologically positive TB patients registered at a clinic in Lusaka, Zambia in 2018

SETTING

An urban TB diagnostic centre in Lusaka, Zambia.

OBJECTIVE

To re-evaluate treatment outcomes of all bacteriologically confirmed TB patients registered in 2018.

DESIGN

This was a retrospective cohort study on TB patients. Treatment outcomes of patients who were transferred out were retrieved.

RESULTS

A total of 182 patients were registered, 26 of whom had missing documents; these were excluded from the study. Of the remaining 156 patients who were reviewed, 86 (55.1%) were correctly evaluated by the centre, 35 (22.4%) were incorrectly evaluated and 35 (22.4%) were 'transferred out' (not evaluated). As a result of this review, the number of evaluated patients increased from 86 (55.1%) to 150 (96.2%). The cure and treatment success rates rose from 43.6% and 44.2%, respectively, to 57.7% and 73.1%, respectively. Of note, 14 of the 35 patients who were initially declared 'transferred out' did not actually reach their treatment facilities and ended up being lost to follow-up.

CONCLUSION

This study shows that it is possible to evaluate almost all TB patients. Re-evaluation of treatment outcomes of TB patients revealed the problems in the TB services that need to be improved in the future.

Structural Insights into the Regulation of Actin Capping Protein by Twinfilin C-terminal Tail

Twinfilin is a conserved actin regulator that interacts with actin capping protein (CP) via C terminus residues (TWtail) that exhibits sequence similarity with the CP interaction (CPI) motif of CARMIL. Here we report the crystal structure of TWtail in complex with CP. Our structure showed that although TWtail and CARMIL CPI bind CP to an overlapping surface via their middle regions, they exhibit different CP-binding modes at both termini. Consequently, TWtail and CARMIL CPI restrict the CP in distinct conformations of open and closed forms, respectively. Interestingly, V-1, which targets CP away from the TWtail binding site, also favors the open-form CP. Consistently, TWtail forms a stable ternary complex with CP and V-1, a striking contrast to CARMIL CPI, which rapidly dissociates V-1 from CP. Our results demonstrate that TWtail is a unique CP-binding motif that regulates CP in a manner distinct from CARMIL CPI.

Crystal structure of human V-1 in the apo form

V-1, also known as myotrophin, is a 13 kDa ankyrin-repeat protein that binds and inhibits the heterodimeric actin capping protein (CP), which is a key regulator of cytoskeletal actin dynamics. The crystal structure of V-1 in complex with CP revealed that V-1 recognizes CP via residues spanning several ankyrin repeats. Here, the crystal structure of human V-1 is reported in the absence of the specific ligand at 2.3 Å resolution. In the asymmetric unit, the crystal contains two V-1 monomers that exhibit nearly identical structures (Cα r.m.s.d. of 0.47 Å). The overall structures of the two apo V-1 chains are also highly similar to that of CP-bound V-1 (Cα r.m.s.d.s of <0.50 Å), indicating that CP does not induce a large conformational change in V-1. Detailed structural comparisons using the computational program All Atom Motion Tree revealed that CP binding can be accomplished by minor side-chain rearrangements of several residues. These findings are consistent with the known biological role of V-1, in which it globally inhibits CP in the cytoplasm.

Ventricular tachycardia in cardiac sarcoidosis -prognosis, characterization of ventricular substrates and outcomes of treatment-

Background

The prognosis, the underlying substrate and clinical outcomes of treatment are unclear in patients with cardiac sarcoidosis (CS)-related ventricular tachycardia (VT).

Objective

This study investigated the prognosis and the relationship between electroanatomical mapping (EAM) and imaging findings in patients with CS-related VT.

Methods

A total of 203 CS patients (Age 68.1±11.6 years, 87 males) were enrolled at two tertiary care medical centers between 2000 and 2018. All met the 2016 Japanese Circulation Society guidelines for diagnosis of CS. They were followed for a composite of major adverse cardiac events (MACE) including cardiac death, heart transplantation, unscheduled hospitalization for heart failure, and life-threatening ventricular arrhythmias. Distribution of late gadolinium enhancement (LGE) on cardiac MRI (CMR) and/or an abnormal myocardial 18F-fluorodeoxyglucose (FDG) uptake on positron emission tomography at diagnosis were examined. The relationship between EAM and the image findings were also analyzed in patients with radiofrequency ablation (RFA) for VT.

Results

During a median follow-up of 53 months, 87 of the 203 patients (43%) experienced a MACE. Baseline factors associated with MACE were presence of sustained VT (HR, 2.43, 95% CI 1.54–3.85, P&lt;0.001), left ventricular ejection fraction below 50% (HR, 1.95 95% CI 1.07–3.56, P=0.029), and abnormal myocardial FDG uptake (HR, 2.42 95% CI 1.04–5.61, P=0.039). Overall, 69 of the 203 patients (34%) experienced sustained VT. Abnormal myocardial FDG uptake was significantly more prevalent in patients with VT than in those without (92.7% vs. 78.5%, P=0.02). A total of 25 patients (9.9%) required RFA for CS-related VT (Age 64.0±8.7 years, 12 males, 1.32±0.56 RFAs per patient). Abnormal electrocardiograms (EGM) were observed in 22 of the 25 patients (88%). LGE was more frequent than abnormal FDG uptake in areas with an abnormal EGM (77% vs. 41%; P=0.002). Over a mean follow-up period of 67-months, 13 of the 25 patients with RFA (52%) remained free of VT episodes (Figure). VT recurred in nine of the 12 patients with RFA and in 17 of the 47 patients without RFA, but was suppressed by intensive pharmacologic therapy such as the combined use of amiodarone and sotalol. In patients with CS-related VT, survival without experiencing a MACE did not differ in participants with or without RFA.

Conclusions

In our 203 CS patients, sustained VT and abnormal FDG uptake were associated with worse cardiac outcomes. The prevalence of abnormal FDG uptake was significantly higher in patients with CS-related VT, LGE on CMR was more frequent within localized areas of an abnormal EGM, suggesting that both scar itself and the associated inflammation were involved in the pathogenesis of CS-related VT. Successful RFA of CS-related VT is still challenging, and recurrence is common. Preprocedural CMR can be useful in detecting abnormal EGMs that are potential targets for substrate ablation.

Funding Acknowledgement

Type of funding source: None

Utility of transcranial color flow imaging for detecting high risk morphology of patent foramen ovale in patients with cerebral infarction

Background

Micro-bubble test by using transcranial color flow imaging (TCCFI) is important as a screening evaluation for diagnosis of paradoxical cerebral embolism which requires the proof of right to left shunt at atrial septum. In addition, high risk features of patent foramen ovale (PFO) that may allow thrombus to easily pass through the PFO itself were previously reported. However, little is known about the association between the degrees on micro-bubble test by TCCFI and the features of high risk PFO.

Purpose

Our aim is to clarify the relationship between the degree of micro-bubble test in TCCFI and the morphology of PFO from transesophageal echocardiography (TEE).

Methods

Seventy-seven patients in whom cardiogenic embolism was strongly suspected by neurologists in Showa University from April to December in 2019 were retrospectively studied. 55 patients underwent both TCCFI and TEE with sufficient Valsalva stress. TCCFI grade of micro-bubble test was classified into 3 groups (A: none, B: small, and C: massive), in which signified “none” is no sign of micro-embolic signals (MES) within 30 seconds, “small” is 1 or more MES, and “massive” is so much MES look like a curtain (Figure). Evaluated high risk characteristics of PFO for cerebral embolism as previously reported were as follows; (1) tunnel height, (2) tunnel length, (3) total excursion distance into right and left atrium, (4) existence of Eustachian valve or Chiari network, (6) angle of PFO from inferior vena cava (7) large shunt (20 or more micro-bubbles).

Results

Of all TCCFI-positive patients (n=32; Group B=19, Group C=13) with cerebral embolism, PFOs were detected in 23 patients in TEE. Therefore, the sensitivity and specificity of TCCFI to PFO were 87% and 63% (AUC=0.75, p&lt;0.001, respectively). Interestingly, all 13 patients (Group C) had manifest PFOs. Moreover, group C include 2 patients with platypnea orthodeoxia syndrome in which hypoxia in the sitting position becomes apparent. Among PFO-positive patients, tunnel height, length, total excursion distance into right and left atrium, and large shunt in TEE were significantly larger in Group C than Group B (p&lt;0.05).

Conclusions

Micro-bubble test by using TCCFI may have screening advantages in predicting paradoxical cerebral embolism, high-risk morphology of PFO, and platypnea orthodeoxia syndrome.

Figure 1

Funding Acknowledgement

Type of funding source: None

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

Knowledge-based structural models of SARS-CoV-2 proteins and their complexes with potential drugs

The World Health Organization (WHO) has declared the coronavirus disease 2019 (COVID‐19) caused by the novel coronavirus SARS‐CoV‐2 a pandemic. There is, however, no confirmed anti‐COVID‐19 therapeutic currently. In order to assist structure‐based discovery efforts for repurposing drugs against this disease, we constructed knowledge‐based models of SARS‐CoV‐2 proteins and compared the ligand molecules in the template structures with approved/experimental drugs and components of natural medicines. Our theoretical models suggest several drugs, such as carfilzomib, sinefungin, tecadenoson, and trabodenoson, that could be further investigated for their potential for treating COVID‐19.

Moderating effect of schizotypy on the relationship between smoking and neurocognition

Purpose

Smoking rates in schizotypic individuals are shown to be elevated, as in patients with schizophrenia, although findings on the association of smoking with different symptomatology of schizotypy have been mixed. Moreover, possible moderating effects of schizotypy on the relationship between smoking and cognition have not been well documented.

Subjects and methods

The Schizotypal Personality Questionnaire (SPQ) and the full version of the Wechsler Memory Scale-Revised (WMS-R) were administered to 501 healthy adults. Subjects were divided into smokers (n = 85) and non-smokers (n = 416) based on the presence/absence of current smoking.

Results

The analysis of covariance (ANCOVA) on the three factor scores as well as the total score of the SPQ, controlling for age and gender, revealed that cognitive-perceptual factor was significantly associated with an increased rate of smoking (P = 0.048). The ANCOVA on the WMS-R indices, with smoking group as a fixed factor and age, gender and total SPQ score as covariates, revealed that the schizotypy-by-smoking interaction was significant for attention/working memory (P = 0.029).

Discussion and conclusion

Positive schizotypy may be associated with more smoking. Schizotypy and smoking could interact with each other to negatively affect attention/working memory.

Pre-treatment lost to follow-up tuberculosis patients, Chongwe, Zambia, 2017: a retrospective cohort study

Setting

Four tuberculosis (TB) diagnostic health facilities of the Chongwe District, Zambia.

Objective

To determine the frequency of bacteriologically confirmed TB patients lost to follow-up (LTFU) before treatment from January to December 2017.

Design

This is a retrospective cohort study involving the review of TB registers. Information on presumptive TB patients who tested positive either by smear microscopy or Xpert^® MTB/RIF assay was extracted from the laboratory TB registers of the TB diagnostic facilities and cross-matched with the TB treatment registers of TB treatment facilities.

Results

Two hundred and seventeen bacteriologically confirmed TB patients were found in the laboratory TB registers. Of these, 145 (67%) were males and seven (3%) were children; 177 (81%) patients were diagnosed using Xpert, while the remaining 40 (19%) were diagnosed using sputum smear microscopy. A total of 71 (33%) were not linked to treatment. Those diagnosed using smear microscopy were 2.5 times (95% CI 1.1-5.3) more likely to be LTFU before treatment than those diagnosed using Xpert.

Conclusion

About one third of TB patients who were not linked to treatment could potentially extend the duration of bacilli transmission in their communities. National TB control programmes should consider including LTFU patients before treatment in routine monitoring and evaluation.

Long-term follow-up of the randomized trial of mesorectal excision with or without lateral lymph node dissection in rectal cancer (JCOG0212)

BACKGROUND

Japan Clinical Oncology Group (JCOG) 0212 (ClinicalTrials.gov NCT00190541) was a non-inferiority phase III trial of patients with clinical stage II-III rectal cancer without lateral pelvic lymph node enlargement. The trial compared mesorectal excision (ME) with ME and lateral lymph node dissection (LLND), with a primary endpoint of recurrence-free survival (RFS). The planned primary analysis at 5 years failed to confirm the non-inferiority of ME alone compared with ME and LLND. The present study aimed to compare ME alone and ME with LLND using long-term follow-up data from JCOG0212.

METHODS

Patients with clinical stage II-III rectal cancer below the peritoneal reflection and no lateral pelvic lymph node enlargement were included in this study. After surgeons confirmed R0 resection by ME, patients were randomized to receive ME alone or ME with LLND. The primary endpoint was RFS.

RESULTS

A total of 701 patients from 33 institutions were assigned to ME with LLND (351) or ME alone (350) between June 2003 and August 2010. The 7-year RFS rate was 71.1 per cent for ME with LLND and 70·7 per cent for ME alone (hazard ratio (HR) 1·09, 95 per cent c.i. 0·84 to 1·42; non-inferiority P = 0·064). Subgroup analysis showed improved RFS among patients with clinical stage III disease who underwent ME with LLND compared with ME alone (HR 1·49, 1·02 to 2·17).

CONCLUSION

Long-term follow-up data did not support the non-inferiority of ME alone compared with ME and LLND. ME with LLND is recommended for patients with clinical stage III disease, whereas LLND could be omitted in those with clinical stage II tumours.

Preparation and evaluation of orally disintegrating tablets containing taste masked microparticles of acetaminophen

In the present work, taste masked particles of acetaminophen (AAP), a highly soluble bitter tasting drug, were developed and ODT containing the taste masked particles were prepared. Taste masked particles of AAP were prepared using different amounts of tetraglycerol polyricinoleate (TGPR) and Eudragit ®E100. Although the drug content ratio and drug recovery decreased with increasing TGPR, drug release from AAP-CR100 particles containing a large amount of TGPR was mostly suppressed for 2 min. Hence, AAP-CR100 was incorporated into ODT as taste masked particles for AAP. Three major disintegrants were used for ODT, and it was confirmed that the tensile strength of all formulations showed applicable hardness for handling. The AAP-CR100-CP(40) formulation containing crospovidone showed the shortest disintegration time and the drug release from AAP-CR100-CP(40) into pH 6.8 test solution was suppressed compared with commercial AAP tablets. Because the drug release from AAP-CR100-CP(40) into the pH 1.2 test solution was rapid, it was suggested that drug release from AAP-CR100-CP(40) is suppressed in the oral cavity, and the drug is released promptly in the stomach. Thus AAP-CR100-CP(40) may be useful as an ODT in which the dissolution of AAP in the oral cavity is suppressed.

All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins

Structural changes of proteins are closely related with their molecular function. We previously developed a computational tool, Motion Tree (MT), to compare protein structures and describe structural changes using solely the Cα atoms. Here, we have extended MT to incorporate all heavy atoms to analyze side chain-related (SCR) motions. All Atom Motion Tree (AAMT) was applied to 76 proteins that exhibited a simple domain motion identified by MT. AAMT also detected 921 SCR motions. We examined the coupling of domain and SCR motions and classified the structural changes in terms of coupling. The statistical results indicated that it is common for coupled SCR motions to also couple with the domain motion. The classification correlates properties of domain motions and SCR motions. The AAMT results suggest that a large domain motion with a sizable domain boundary is accompanied by SCR motions composed of more than a single residue, which induces further couplings of SCR motions.

Protein kinases phosphorylate long disordered regions in intrinsically disordered proteins

Phosphorylation is a major post-translational modification that plays a central role in signaling pathways. Protein kinases phosphorylate substrates (phosphoproteins) by adding phosphate at Ser/Thr or Tyr residues (phosphosites). A large amount of data identifying and describing phosphosites in phosphoproteins has been reported but the specificity of phosphorylation is not fully resolved. In this report, data of kinase-substrate pairs identified by the Kinase-Interacting Substrate Screening (KISS) method were used to analyze phosphosites in intrinsically disordered regions (IDRs) of intrinsically disordered proteins. We compared phosphorylated and nonphosphorylated IDRs and found that the phosphorylated IDRs were significantly longer than nonphosphorylated IDRs. The phosphorylated IDR is often the longest IDR (71%) in a phosphoprotein when only a single phosphosite exists in the IDR, and when the phosphoprotein has multiple phosphosites in an IDR(s), the phosphosites are primarily localized in a single IDR (78%) and this IDR is usually the longest one (81%). We constructed a stochastic model of phosphorylation to estimate the effect of IDR length. The model that accounted for IDR length produced more realistic results when compared with a model that excluded the IDR length. We propose that the IDR length is a significant determinant for locating kinase phosphorylation sites in phosphoproteins.

Trends of tuberculosis rates before and after the declaration as a public health emergency in Japan, 1992–2006

SETTING: Over the period 1992 to 2006, Japan had tuberculosis (TB) notification rates of about 40 to 20 per 100 000 population. In 1999, the Minister of Health and Welfare of Japan declared a public health emergency based on the resurgence of TB.OBJECTIVE: To compare the trends of TB notification rates before and after the declaration.DESIGN: This is an ecological study on the trends of TB notification rates. The trends per year in TB notification rates were compared before (1992–1997) and after (2001–2006) the emergency declaration.RESULTS: The trends in the notification rates for all types of TB and sputum smear-positive TB (SSP-TB) decreased from −3.3% (95% confidence interval [CI] −4.6 to −1.9) and 0.94% (95%CI −0.33 to 2.2), respectively, per year before the declaration to −5.8% (95%CI −6.3 to −5.3) and −3.3% (95%CI −2.4 to −4.2), respectively, per year after the declaration with statistical significance. Trends in notification rates for both all types of TB and SSP-TB statistically significantly decreased after the declaration in Fukuoka, Osaka and Saitama Prefectures.CONCLUSION: The declaration of TB as a public health emergency in Japan in 1999 had a positive impact on TB control in Japan and thus TB epidemiology.

Using 1 HN amide temperature coefficients to define intrinsically disordered regions: An alternative NMR method

This report describes a cost-effective experimental method for determining an intrinsically disordered protein (IDP) region in a given protein sample. In this area, the most popular (and conventional) means is using the amide (¹ H^N ) NMR signal chemical shift distributed in the range of 7.5-8.5 ppm. For this study, we applied an additional step: analysis of ¹ H^N chemical shift temperature coefficients (¹ H^N -CSTCs) of the signals. We measured ¹ H-¹⁵ N two-dimensional NMR spectra of model IDP samples and ordered samples at four temperatures (288, 293, 298, and 303 K). We derived the ¹ H^N -CSTC threshold deviation, which gives the best correlation of ordered and disordered regions among the proteins examined (below -3.6 ppb/K). By combining these criteria with the newly optimized chemical shift range (7.8-8.5 ppm), the ratios of both true positive and true negative were improved by approximately 19% (62-81%) compared with the conventional "chemical shift-only" method.

Tuberculosis-related technical enquiries received by a national level institution in Japan, 2014-2016

Background: Japan had a tuberculosis (TB) notification rate of 13.9 per 100 000 population in 2016. Objectives: To characterise TB-related enquiries received by the Research Institute of Tuberculosis, Tokyo, Japan, between January 2014 and December 2016. Design: A descriptive study of the time, place and other attributes of the enquiries. Results: A total of 1864 enquiries were listed for analysis. On average, 51.8 enquiries (range 30-77) were received per month. The enquiry rates were highest for Yamanashi (5.87/100 000) and Kochi (5.77) Prefectures, and lowest in Miyazaki (0.45) and Saga (0.48) Prefectures. Enquirers belonged mostly to local governments (n = 1212, 65%) and health care facilities (n = 386, 21%), and included medical doctors (n = 412, 22%), nurses (n = 926, 50%) and the general public (n = 150, 8.0%). Most enquiries concerned TB diagnosis and treatment (n = 475, 25%), including diagnosis in general (n = 38, 2.0%), laboratory diagnosis (n = 83, 4.5%), anti-tuberculosis treatment in general (n = 62, 3.3%) and the management of comorbidities or adverse events (n = 60, 3.2%), followed by contact investigations (n = 371, 20%). Conclusions: As most enquiries concerned the diagnosis and treatment of TB, the Ministry of Health of Japan should maintain a number of specialised TB institutions with TB clinicians to provide technical assistance.

Randomized clinical trial of high versus low inferior mesenteric artery ligation during anterior resection for rectal cancer

BACKGROUND

The optimal level for inferior mesenteric artery ligation during anterior resection for rectal cancer is controversial. The aim of this randomized trial was to clarify whether the inferior mesenteric artery should be tied at the origin (high tie) or distal to the left colic artery (low tie).

METHODS

Patients were allocated randomly to undergo either high- or low-tie ligation and were stratified by surgical approach (open or laparoscopic). The primary outcome was the incidence of anastomotic leakage. Secondary outcomes were duration of surgery, blood loss and 5-year overall survival.

RESULTS

Some 331 patients entered the trial between June 2006 and September 2012. The trial was stopped prematurely as recruitment was slow. Seven patients were excluded after randomization but before operation because of procedural changes. High tie and low tie were performed in 164 and 160 patients respectively. The incidence of anastomotic leakage was not significantly different (17·7 versus 16·3 per cent respectively; P = 0·731). The incidence of severe complications requiring intervention was 2·4 versus 5·0 per cent for high and low tie respectively (P = 0·222). In multivariable analysis, risk factors for anastomotic leakage included male sex (odds ratio 4·36, 95 per cent c.i. 1·56 to 12·18) and distance of the tumour from the anal verge (odds ratio 0·99, 0·98 to 1·00). At 5 years there were no significant differences in overall (87·2 versus 89·4 per cent respectively; P = 0·386) and disease-free (76·3 versus 77·6 per cent; P = 0·765) survival.

CONCLUSION

The level of ligation of the inferior mesenteric artery does not significantly influence the rate of anastomotic leakage. Registration number: NCT01861678 ( https://clinicaltrials.gov).