The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection.

Genetic mechanisms influencing COVID-19 susceptibility are not well understood. Here, the authors analyzed whole blood RNA-seq data of 465 Japanese individuals with COVID-19, highlighting thousands of fine-mapped variants affecting expression and splicing of genes, as well as the presence of COVID-19 severity-interaction eQTLs.

Prolonged viral shedding of SARS-CoV-2 in an immunocompromised patient

The duration of viral shedding of SARS-CoV-2 is usually less than 10 days. We experienced a COVID-19 case with prolonged viral shedding for 2 months. His cell mediated immunity has been depressed (CD4⁺T cell <100/μl) due to advanced malignant lymphoma and chemotherapy which had been completed 4 months prior to the onset of symptoms of COVID-19. We administered several treatments against COVID-19, however the results of Polymerase Chain Reaction (PCR) from nasopharyngeal specimens remained positive to SARS-CoV-2 for 2 months. Moreover, virus isolation assays performed on Day 59 also remained positive. He was finally discharged on Day 69 with two consecutive negative PCR results for SARS-CoV-2. Immunocompromised status may prolong viral shedding and it is therefore important for the clinician to take into account this when assessing such patients.

Basement membrane zone IgE deposition is associated with bullous pemphigoid disease severity and treatment results

BACKGROUND

A subset of patients with bullous pemphigoid (BP) show deposition of IgE in the basement membrane zone (BMZ), yet the relationship between BMZ IgE and the clinical presentation of BP remains unclear.

OBJECTIVES

To investigate the relationship between IgE deposition, IgE levels in serum, and disease severity in patients with BP.

METHODS

We investigated IgE autoantibodies in 53 patients with BP by direct immunofluorescence (DIF), indirect immunofluorescence and enzyme-linked immunosorbent assay.

RESULTS

Of 53 patients with BP, 23 (43%) had IgE deposition, 10 (19%) of whom were IgE+ and 13 (25%) IgE± according to DIF analyses. Erosion/blister (E/B) Bullous Pemphigoid Disease Area Index (BPDAI) scores were significantly higher in IgE+ patients than in IgE- patients (n = 15), while no significant differences were found for urticaria/erythema BPDAI scores. IgE+ and IgE± patients took longer to reduce their E/B BPDAI score by 75% after systemic corticosteroid treatment. BP180-IgE levels were significantly higher among IgE+ patients than IgE± or IgE- patients (n = 10). Total IgE levels in the serum and blood eosinophil counts did not differ between IgE+, IgE± and IgE- patients. A significant correlation was detected between BP180-IgG and BP180-IgE, but not between BPDAI scores and any of BP180-IgG, BP180-IgE or blood eosinophil count.

CONCLUSIONS

IgE deposition in the BMZ is associated with higher E/B BPDAI scores and longer treatment periods. We conclude that IgE binding in the BMZ may contribute to BP pathogenesis by promoting blister formation. What's already known about this topic? BP180-IgE autoantibodies have an important role in the pathogenesis of bullous pemphigoid (BP). A subset of patients with BP display deposition of IgE within the basement membrane zone (BMZ) of skin tissue. What does this study add? Patients with in vivo IgE deposition in the BMZ displayed higher erosion/blister Bullous Pemphigoid Disease Area Index (BPDAI) scores, while urticaria/erythema BPDAI scores were not significantly different. Patients with in vivo IgE deposition in the BMZ took longer to reduce their erosion/blister BPDAI score by 75% after systemic corticosteroid treatment. BP180-specific IgE levels in serum were higher among patients with linear IgE deposition in the BMZ than in those with granular or no IgE deposition.

Feasibility Evaluation of Smart Stretcher to Improve Patient Safety during Transfers

Objectives: The integration of noninvasive vital sign sensors and wireless sensor networks into intelligent alarm systems has the potential to improve patient safety. We developed a wireless network-based system (“Smart Stretcher”), which was designed to constantly monitor patient vital signs and detect apnea during transfers within a hospital. The system alerts medical staff in case of an emergency through a wireless network.

Methods: A small-scale technical feasibility study was conducted to assess the performance of the system in a simulated hospital environment. Smart Stretcher consists of three components: a small air-mat type pressure sensor measuring respiratory rate and detecting apnea, a patient identification system using RFID technology, and an indoor positioning system using a ZigBee wireless network. In the feasibility experiment, two nurses transferred four subjects who stopped breathing for 10 seconds, after which we calculated the accuracy of apnea detections, repeating this at varying speeds and subject positions. We alsoperformed asubjective evaluation of perceptions and expectations of Smart Stretcher by nurses.

Results: The system could detect apnea in all subjects at a rate of over 90%, patient IDs and locations were correctly detected in real time, and the system could alert medical staff. In addition, the results of nurse’s evaluations were mostly positive.

Conclusions: The technical feasibility experiment and evaluation of Smart Stretcher suggest that the system could play a key role in monitoring patients during hospital transfers.

Revision of the Massarineae (Pleosporales, Dothideomycetes)

We here taxonomically revise the suborder Massarineae (Pleosporales, Dothideomycetes, Ascomycota). Sequences of SSU and LSU nrDNA and the translation elongation factor 1-alpha gene (tef1) are newly obtained from 106 Massarineae taxa that are phylogenetically analysed along with published sequences of 131 taxa in this suborder retrieved from GenBank. We recognise 12 families and five unknown lineages in the Massarineae. Among the nine families previously known, the monophyletic status of the Dictyosporiaceae, Didymosphaeriaceae, Latoruaceae, Macrodiplodiopsidaceae, Massarinaceae, Morosphaeriaceae, and Trematosphaeriaceae was strongly supported with bootstrap support values above 96 %, while the clades of the Bambusicolaceae and the Lentitheciaceae are moderately supported. Two new families, Parabambusicolaceae and Sulcatisporaceae, are proposed. The Parabambusicolaceae is erected to accommodate Aquastroma and Parabambusicola genera nova, as well as two unnamed Monodictys species. The Parabambusicolaceae is characterised by depressed globose to hemispherical ascomata with or without surrounding stromatic tissue, and multi-septate, clavate to fusiform, hyaline ascospores. The Sulcatisporaceae is established for Magnicamarosporium and Sulcatispora genera nova and Neobambusicola. The Sulcatisporaceae is characterised by subglobose ascomata with a short ostiolar neck, trabeculate pseudoparaphyses, clavate asci, broadly fusiform ascospores, and ellipsoid to subglobose conidia with or without striate ornamentation. The genus Periconia and its relatives are segregated from the Massarinaceae and placed in a resurrected family, the Periconiaceae. We have summarised the morphological and ecological features, and clarified the accepted members of each family. Ten new genera, 22 new species, and seven new combinations are described and illustrated. The complete ITS sequences of nrDNA are also provided for all new taxa for use as barcode markers.

Alterations in time intervals of ductus venosus and atrioventricular flow velocity waveforms in growth-restricted fetuses

OBJECTIVE

To investigate time intervals of the ductus venosus (DV) flow velocity waveform (FVW) and those of the cardiac cycle that correspond with each DV-FVW component in fetuses with intrauterine growth restriction (IUGR) due to placental insufficiency.

METHODS

Women with a pregnancy complicated by IUGR were recruited into the study, as was a normal control group. Time intervals for systolic (S) and diastolic (D) components were measured in DV-FVW as follows: S(DV), from the nadir of the a-wave during atrial contraction to the nadir between the S-wave and D-wave; D(DV), from the nadir between S-wave and D-wave to the nadir of the a-wave. Regarding cardiac cycles, the following variables were measured from ventricular inflow through the tricuspid valve (TV) and mitral valve (MV): S(TV) and S(MV), from the second peak of ventricular inflow caused by atrial contraction (A-wave) to the opening of the atrioventricular valve; D(TV) and D(MV), from the opening of the atrioventricular valve to the peak of the A-wave. In the IUGR group, only the last examination performed within 1 week of delivery was used for analysis. All variables were analyzed statistically using Z-scores.

RESULTS

Data were obtained from 249 normal fetuses and 26 fetuses with IUGR. Compared to normal fetuses, S(DV) showed a significant decrease (P < 0.001), while D(DV) showed a significant increase (P < 0.001) in the IUGR group. Regarding cardiac cycles, S(TV) and S(MV) showed significant decreases (P = 0.014 and P < 0.001, respectively) and D(TV) and D(MV) showed significant increases (P = 0.008 and P = 0.002, respectively) in fetuses with IUGR.

CONCLUSION

Time-interval alterations of DV-FVW in growth-restricted fetuses reflect the hemodynamic events caused by placental insufficiency.

Time-interval analysis of ductus venosus flow velocity waveforms in twin-to-twin transfusion syndrome treated with laser surgery

OBJECTIVES

To investigate time-interval variables of ductus venosus (DV) flow velocity waveforms (FVWs) in twin-to-twin transfusion syndrome (TTTS), comparing the results with reference ranges from normal singleton fetuses. The impact of laser surgery and the effect of prognostic factors were also evaluated.

METHODS

In 107 TTTS cases, DV-FVWs of both recipients and donors were recorded 1 day before and 2 days after laser therapy. Time intervals for systolic (S) and early diastolic (D) peaks were analyzed retrospectively with regard to acceleration time (acc-S and acc-D for S and D, respectively) and deceleration time (dec-S and dec-D for S and D, respectively). For each variable, Z-scores were calculated with respect to previously reported normal reference ranges.

RESULTS

Z-scores for all variables showed statistically significant differences from those observed previously in normal fetuses, with the exception of dec-S of donors. The most striking differences were observed in longer dec-S of recipients (P < 0.001) and longer dec-D of donors (P < 0.001). Laser therapy showed significant impact on dec-S and acc-D in recipients and on all variables in donors. Regarding the short-term prognosis, acc-S and dec-S showed significant differences for the prediction of intrauterine fetal demise in donors (P = 0.009 and P = 0.011, respectively).

CONCLUSION

This study demonstrates that time-interval variables of DV-FVWs may differentiate the characteristic hemodynamic changes caused by unbalanced blood volume between recipients and donors.

New methods for species and sex determination in three sympatric Mustelids, Mustela itatsi, Mustela sibirica and Martes melampus

We developed novel species and sex determination methods for three Japanese mustelid species. We used DDX3Y to determine sex and generated a primer set to amplify both DDX3X and DDX3Y DNA in Mustela itatsi, M. sibirica and Martes melampus. To determine species and sex simultaneously, we generated fluorescence-labelled primers that give different fragment lengths at D-loop, DDX3X and DDX3Y of these three species using a DNA sequencer.

Topical application of PPARα (but not β/δ or γ) suppresses atopic dermatitis in NC/Nga mice

BACKGROUND

Peroxisome proliferator-activated receptors (PPARs) are nuclear receptors, which regulate not only adipogenesis and proliferation/differentiation but also the immune response of cells. Because topical application of the activators of some PPAR isoforms improved clinical symptoms in patients with atopic dermatitis (AD), we investigated the role of PPAR activators using a murine AD model in NC/Nga mice; to the best of our knowledge, this has not been previously reported.

METHODS

Activators of three PPAR isoforms (α, β/δ, γ) were topically applied on inflamed skin in a murine AD model that was developed by repeated topical application of mite antigen in NC/Nga mice. The efficacy of each topical PPAR activator was evaluated immunologically and serologically.

RESULTS

Topical application of the PPARα activator, but not of the activators of PPARβ/δ or PPARγ, improved clinical dermatitis, reduced inflammatory cell infiltration in the dermis, and alleviated the elevation of serum IgE levels. In addition, PPARα expression was downregulated in the epidermis in our murine AD model, as is seen in patients with AD.

CONCLUSIONS

Topical application of PPARα activator could be a potent therapeutic agent for patients with AD and could take the place of topical steroid treatments.

[A case of slowly progressive type 1 diabetes mellitus developing myeloperoxidase-specific anti-neutrophil cytoplasmic antibody-associated vasculitis with hypertrophic pachymeningitis manifesting as multiple cranial nerve palsy]

We report a 63-year-old man with a 35-year history of slowly progressive type 1 diabetes mellitus (SPIDDM), complicated with myeloperoxidase-specific anti-neutrophil cytoplasmic antibody (MPO-ANCA)-associated vasculitis presenting alveolar hemorrhage and pachymeningitis. The patient was first diagnosed as having DM at age of 28 years old and deteriorated secretion of insulin and the typical clinical course led us to the diagnosis of SPIDDM. When he was 58 years old, he suffered from fever, headache, and alveolar hemorrhage. He was diagnosed as having MPO-ANCA associated vasculitis based on a high titer of MPO-ANCA and histological findings of lung biopsy. Treatment with steroid pulse therapy, followed by oral prednisolone and oral cyclophosohamide, resulted in clinical improvement. Five years later, he complained of double vision. A gadolinium-enhanced magnetic resonance imaging (MRI) study of the brain showed normal. Two months later, he developed right cranial nerve V~XII palsy. A second MRI study revealed thickening of the right temporal region and cerebellar dura mater, leading us to the diagnosis of hypertrophic pachymeningitis. He responded well to oral prednisolone (50 mg/day) and intravenous cyclophosohamide (500 mg). This is the first case report of SPIDDM complicated with MPO-ANCA-associated vasculitis, manifesting as alveolar hemorrhage and hypertrophic pachymeningitis.

[A case of calcinomatous polyarthritis presenting rheumatoid arthritis-like polyarthritis as the initial symptom of gastric cancer]

We report a case of calcinomatous polyarthritis presenting rheumatoid arthritis-like polyarthritis as the initial symptom of gastric cancer. A 79-year-old male visited to our hospital with complaint of pain and swelling of multiple joints including bilateral hands, bilateral knees, elbows and small joints of fingers. He also complained of neck and back stiffness. Both of rheumatoid factor test and anti-cyclic citrullinated peptide antibody were negative. Non-steroidal anti-inflammatory drug did not relieve his arthritic pain. He showed anorexia, body weight loss and was anemic. Upper gastrointestinal endoscopic evaluation demonstrated a gastric cancer. The patient underwent subtotal gastrectomy. Within 1 week after the subtotal gastrectomy, both polyarthritis and stiffness started to improve. The polyarthritis in this case was diagnosed as calcinomatous plyarthritis for its features. Paraneoplastic rheumatism remains a rare event, but knowledge of it is essential for early diagnosis of underlying cancer.

Polymyositis associated with autoimmune hepatitis, primary biliary cirrhosis, and autoimmune thrombocytopenic purpura

We describe a 40-year-old woman with polymyositis (PM) who developed autoimmune hepatitis (AIH), primary biliary cirrhosis (PBC), and autoimmune thrombocytopenic purpura (AITP) concurrently. About 4 years earlier, she suffered from muscle weakness probably due to PM. When she visited our hospital, she had polyarthritis, myalgia, symmetrical proximal limb-muscle weakness, elevated muscle enzymes, and myogenic abnormalities on electromyogram. Pathological findings obtained by muscle biopsy showed histological findings consistent with PM. Her serum liver enzymes were also elevated. The histology obtained by liver biopsy revealed the mixture findings of chronic active hepatitis and biliary cirrhosis. As antibodies to mitochondria M2 and liver/kidney microsome type 1 (LKM-1) were present, we concluded her liver disease was due to an overlap of AIH and PBC. Furthermore, purpura on the legs with thrombocytopenia appeared in parallel with liver dysfunction. She was diagnosed as having AITP by clinical and laboratory findings. Her serum showed a speckled pattern in immunofluorescence antinuclear antibody testing, but the antigen specificities were distinct from those of the known myositis-related autoantigens. This is a first case report of PM accompanied by AIH, PBC, and AITP. It was notable that there was an overlap of disease-associated immunological findings and immunogenetic backgrounds. This case provides a possible insight into the mechanisms and interplay of autoimmune diseases.

Identification of N-homocysteinylated apolipoprotein AI in normal human serum

Background

In human serum, a portion of homocysteine (Hcy) exists as an N-linked form to the ε-amino group of protein lysine residues. N-homocysteinylated proteins differ structurally and functionally from native proteins. The present study strives to develop detection and potential semi-quantification methods for N-homocysteinylated apolipoprotein AI ( N-Hcy-apoAI) in human serum.

Methods

Serum treated with or without cysteamine was supplied to isoelectric focusing (IEF) followed by an immunoblot using an anti-apoAI antibody. Cysteamine treatment increased the isoelectric point for N-Hcy-apoAI, but not for unmodified apoAI, due to the presence of -SH group(s) derived from Hcy and the absence of a cysteine residue in the apoAI molecule. N-Hcy-apoAI was semi-quantified from the scanned immunoblot pattern via a computer.

Results

After cysteamine treatment, N-Hcy-apoAI in the serum was identified by IEF at the position with a higher pI value compared with intact apoAI. The reproducibility (between assays) of the semi-quantification method was 19.1% CV (coefficient of variation) for an average ratio 5.9% of N-Hcy-apoAI to the whole apoAI in the serum. Approximately 1.0–7.4% of apoAI was N-homocysteinylated in the serum obtained from 27 healthy subjects. Neither the ratio of N-Hcy-apoAI nor its concentration, calculated by total apoAI concentration, indicated correlation with the so-called total (free and S-linked) Hcy concentration.

Conclusions

We directly found that a portion of apoAI in the serum undergoes homocysteinylation in an N-linkage manner, and used this to develop a potential semi-quantification method for N-Hcy-apoAI.

Step-up therapy with biphasic insulin aspart-70/30--Sapporo 1-2-3 study

The effectiveness of BIAsp 30 step-up therapy in achieving glycemic control in Japanese patients with type 2 diabetes mellitus was investigated. Study subjects were 99 patients with type 2 diabetes mellitus aged over 20 years who were judged to require insulin therapy due to poor glucose control (HbA1c level of > or =7.5%). BIAsp 30 dosage was determined by the patient's attending physician; coadministration of hypotensive agents and antilipemic agents was permitted, but OAD coadministration was limited to patients already receiving such drugs at the start of the study. Patients who did not achieve HbA1c <6.5% after 16+/-5 weeks with QD (Phase 1) were stepped up to BID (Phase 2). If patients still had not achieved HbA1c <6.5% after 16+/-5 weeks with BID, they were stepped up to TID (Phase 3). 55 of the 99 enrolled subjects completed the study and the rates of achievement of HbA1c <6.5% and HbA1c <7.0% were 45.5% and 74.5%, respectively. Of all registered subjects, 5.1% (5/99) achieved HbA1c <6.5% in QD, 19.5% (16/82) in BID, and 20.6% (7/34) in TID. Statistically significant reductions in HbA1c levels were recorded at the conclusion of each phase, with no incidents requiring intervention, indicating that BIAsp 30 step-up therapy is a safe, simple therapy that can be useful in achieving better glycemic control for Japanese patients with type 2 diabetes mellitus.

[A case report of a HIV-infected patient, who was denied to return home because of his psychological complications along with hepatocellular carcinoma]

Although a social support system has been developed in recent times, some of the difficult cases which complicate serious diseases due mainly to lack of family care power, have been reported. We experienced one HIV-infected patient who suffered from hepatic carcinoma and had been taken care of at home, but he was denied to return home after hospitalization. It has been reported that the management of homecare station has become worsened and the number of stations has been decreasing in various locations. If the patients were selected by homecare stations in which the management was going from bad to worse, it would be difficult to maintain a nationwide quality of homecare system. By presenting such an extreme case in the homecare services, we propose a homecare scoring system, in consideration of homecare service limitations, which will be helpful assessing a difficult case of a patient taken care of at home.