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.

Frequency and Significance of Coinfection in Patients with COVID-19 at Hospital Admission.

Objective Viral pneumonia is not rare in community-acquired pneumonia (CAP). Mixed or secondary pneumonia (coinfection) can be seen in viral pneumonia; however, its frequency in coronavirus disease 2019 (COVID-19) has only been investigated in a few studies of short duration, and its significance has not been fully elucidated. We investigated the frequency and significance of co-infection in patients with COVID-19 over a 1-year study period. Methods Coinfection was investigated via multiplex polymerase chain reaction (PCR), culture of respiratory samples, rapid diagnostic tests, and paired sera. We used logistic regression analysis to analyze the effect of coinfection on severity at admission and Cox proportional-hazards model analysis to analyze the effect of coinfection on need for high-flow nasal cannula, invasive mandatory ventilation use, and death, respectively. Patients We retrospectively investigated 298 patients who suffered CAP due to severe acute respiratory syndrome coronavirus-2 infection diagnosed by PCR and were admitted to our institution from February 2020 to January 2021. Results Primary viral pneumonia, and mixed viral and bacterial pneumonia, accounted for 90.3% and 9.7%, respectively, of COVID-19-associated CAP, with viral coinfection found in 30.5% of patients with primary viral pneumonia. Influenza virus was the most common (9.4%). Multivariable analysis showed coinfection not to be an independent factor of severity on admission, need for high-flow nasal cannula or invasive mandatory ventilation, and mortality. Conclusion Viral coinfection was common in COVID-19-associated CAP. Severity on admission, need for high-flow oxygen therapy or invasive mandatory ventilation, and mortality were not affected by coinfection.

Characteristics of pulmonary cryptococcosis in patients with rheumatoid arthritis.

BACKGROUND AND OBJECTIVE: A high frequency of infections complicating rheumatoid arthritis (RA) has been reported due to the immunomodulatory effect of RA or to agents with immunosuppressive effects used in its treatment. We aimed to assess clinical and radiological characteristics of pulmonary cryptococcosis in patients with and without RA. METHODS: We retrospectively reviewed the medical records of 52 patients with pulmonary cryptococcosis and divided them into two groups, those with RA and without RA, and compared clinical characteristics and radiological findings between them. RESULTS: Eleven (21.2%) of the 52 patients had RA. Median follow-up periods were 51.2 (range: 1.1-258.7) months for patients with RA and 19.1 (range: 0.63-246.9) months for patients without RA. Among the patients with RA, 81.8% were women, with a mean age of 68.1 years. Female sex and respiratory comorbidities were significantly more frequent in patients with RA than in patients without RA. Frequencies of concomitant cryptococcal meningitis and respiratory failure were not different between the groups. There were no significant differences in frequency of any radiological findings, locations and number between the two groups. Among patients with RA, all but one responded well to antifungal treatment. During the antifungal treatment course, one (9.1%) patient with RA died of cryptococcosis. Despite continuing antirheumatic drugs, no patients had recurrence of pulmonary cryptococcosis during follow-up. CONCLUSION: Other than some differences in background, there were no clinical, radiological or prognostic differences between the patients with and without RA with pulmonary cryptococcosis. The administration of antirheumatic therapy had no negative effect on the clinical course of antifungal treatment.

Rheumatoid Arthritis Accompanying Diffuse Panbronchiolitis.

A 58-year-old woman with rheumatoid arthritis (RA) visited our hospital complaining of a persistent cough and sputum for the past year. She had a high cold hemagglutinin titer and chronic sinusitis. Chest computed tomography revealed bilateral diffuse centrilobular nodules, bronchiectasis, and bronchial wall thickening. A surgical lung biopsy was performed that confirmed diffuse panbronchiolitis (DPB) because of the lymphocytic and plasmacytic infiltrates in the respiratory bronchioles. Her condition improved after the administration of clarithromycin. Several cases of RA complicating DPB have previously been reported, but only in Japan. We need to consider DPB as a bronchiolitis types accompanying RA among Japanese patients.

A retrospective analysis of pembrolizumab plus chemotherapy versus pembrolizumab monotherapy for advanced or recurrent non-small cell lung cancer.

BACKGROUND: Although clinical trials have investigated the addition of pembrolizumab to chemotherapy for non-small cell lung cancer, none have investigated the addition of chemotherapy to pembrolizumab. METHODS: We conducted a retrospective study of 71 NSCLC patients including 33 treated with pembrolizumab plus chemotherapy (combination therapy group) and 38 treated with pembrolizumab monotherapy (monotherapy group) from 1 May 2016 to 31 August 2020. RESULTS: Eleven of 33 (33.3%) patients in the combination therapy group and 37 of 38 (97.4%) patients in the monotherapy group had programmed cell death ligand-1 (PD-L1) tumor proportion score (TPS) ≥50%. Objective response rate (ORR) and median overall survival (OS) were not significantly different between the combination therapy group and monotherapy group (54.5% vs. 47.4, p = 0.637 and 16.6 vs. 27.0 months, p = 0.463). In patients with PD-L1 TPS ≥50%, ORR and median OS were not different between the combination therapy group and the monotherapy group (63.6% vs. 48.6%, p = 0.499 and not reached vs. 27.0 months, p = 0.976). Thirty-three (100%) patients experienced adverse events (AEs) in the combination therapy group and 32 (84.2%) in the monotherapy group. Treatment discontinuation at 1 year due to AEs occurred more frequently in the combination therapy group (45.2%) than in the monotherapy group (21.1%). CONCLUSION: There was no significant difference in ORR and OS between the two groups, and treatment discontinuation was more frequent in the combination group. A randomized controlled trial is needed to evaluate the addition of chemotherapy to pembrolizumab for first-line treatment in patients with PD-L1 TPS ≥50%.

Outcome and risk factor of immune-related adverse events and pneumonitis in patients with advanced or postoperative recurrent non-small cell lung cancer treated with immune checkpoint inhibitors.

BACKGROUND: Non-small cell lung cancer (NSCLC) patients with pre-existing respiratory diseases have been excluded in clinical trials of immune checkpoint inhibitor (ICI) therapy, and it is unknown whether the same degree of response can be expected as that in patients without pre-existing respiratory diseases and if they are associated with increased risk for various immune-related adverse events (irAEs) and ICI pneumonitis. This study aimed to evaluate predictive factors of clinical response, prognostic factors, risk factors of irAEs, and ICI pneumonitis in NSCLC patients with or without pre-existing respiratory diseases. METHODS: We conducted a retrospective study of 180 NSCLC patients who received ICI monotherapy of nivolumab, pembrolizumab, or atezolizumab from 1 January 2016 to 31 March 2019. RESULTS: A total of 119 patients had pre-existing respiratory diseases, including 20 with pre-existing idiopathic interstitial pneumonias (IIPs). A total of 85 patients experienced irAEs, of which ICI pneumonitis was the most frequent adverse event, occurring in 27 patients. Of the three patients who died from irAEs, all from ICI pneumonitis, two had pulmonary emphysema and one had pre-existing IIP. In multivariate analyses, irAEs were associated with objective response rate (ORR) and favorable OS, and IIPs were associated with increased risk for ICI pneumonitis. However, IIPs were not associated with low ORR or poor OS. CONCLUSIONS: Pre-existing IIPs were a risk factor for ICI pneumonitis. However, this study showed that ICI therapy can be offered to patients with pre-existing respiratory diseases with the expectation of the same degree of response as that in patients without pre-existing respiratory diseases. KEY POINTS: Significant findings of the study: Pre-existing IIPs were a risk factor for ICI pneumonitis, but objective response rate and prognosis of patients with IIPs were similar to those of other patients. WHAT THIS STUDY ADDS: In patients with pre-existing IIPs, ICI pneumonitis should be noted. However, ICI therapy can be offered to patients with pre-existing respiratory diseases with the expectation of the same degree of response as that in patients without pre-existing respiratory diseases.

Clinical course and findings of 14 patients with COVID-19 compared with 5 patients with conventional human coronavirus pneumonia.

OBJECTIVE: To clarify what future problems must be resolved and how clinical findings of SARS-CoV-2 infection differ from those of cHCoV infection. METHODS: Patients and Methods Clinical characteristics of 14 patients with laboratory-confirmed Coronavirus disease 2019 (COVID-19) and 5 patients with cHCoV pneumonia admitted to our institution and treated up to March 8, 2020, were retrospectively analyzed. RESULTS: On admission, 10 patients had pneumonia, 5 of whom had pulmonary shadows detectable only via computed tomography (CT). During hospitalization, another patient with no pulmonary shadows on admission developed pneumonia. In total, 11 (78.6%) of the 14 patients developed pneumonia, indicating its high prevalence in COVID-19. During hospitalization, the patients' symptoms spontaneously relapsed and resolved, and gastrointestinal symptoms were frequently found. C-reactive protein values showed correlation with the patients' clinical courses. Ritonavir/lopinavir were administered to 5 patients whose respiratory conditions worsened during admission, all of whom improved. However, the pneumonia in the 6 other patients improved without antivirals. None of the 14 patients died, whereas 5 other patients with cHCoV pneumonia were in respiratory failure on admission, and one patient (20%) died. CONCLUSION: Both SARS-CoV-2 and cHCoV can cause severe pneumonia. Problems for future resolution include whether antiviral agents administered in cases of mild or moderate severity can reduce the number of severe cases, and whether antivirals administered in severe cases can reduce mortality.

Remitting Seronegative Symmetrical Synovitis with Pitting Edema Syndrome Complicated with Organizing Pneumonia.

We herein report a 62-year-old man with idiopathic pulmonary fibrosis who developed remitting seronegative symmetrical synovitis with pitting edema (RS3PE) syndrome during follow-up. Pulmonary infiltrations were detected concomitantly with the development of RS3PE syndrome, and prednisolone improved both the pulmonary and extrapulmonary lesions. Recognizing the pulmonary manifestations of RS3PE syndrome is necessary to provide an appropriate diagnosis and disease management.

A case of invasive pulmonary aspergillosis diagnosed by transbronchial lung biopsy during treatment for diabetic ketoacidosis in a type 1 diabetic patient.

Invasive pulmonary aspergillosis (IPA) patients with non-hematological malignancy are far less than with hematological malignancy patients. We encountered a very rare case of IPA in which type 1 diabetes was the only conceivable risk factor. Further, according to the diagnostic categories of the European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) criteria for IPA, the frequency of proven diagnosis is very low. Here we report a proven IPA, which rapidly developed when the patient with type 1 diabetes was being treated for diabetic ketoacidosis, which was successfully treated with the combination therapy of voriconazole (VRCZ) and micafungin (MCFG), based on early diagnosis using bronchoscopy.

Spontaneous regression of primary endobronchial extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue.

Extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma) of pulmonary origin is a relatively rare disease. In particular, reports of MALT lymphoma occurring and localized in the trachea or bronchus have been limited. Pulmonary MALT lymphoma has been reported to demonstrate spontaneous regression, whereas there is only one reported case of spontaneous regression of primary endobronchial MALT lymphoma. We herein report the case of a 70-year-old man with primary endobronchial MALT lymphoma who showed spontaneous regression with an interest of endobronchial findings.

Pulmonary alveolar proteinosis developing during steroid treatment in a patient with organizing pneumonia in association with atypical chronic myeloid leukemia.

Organizing pneumonia (OP) and pulmonary alveolar proteinosis (PAP) are rare complications in patients with hematologic disorders. We herein report a case of PAP that developed during steroid treatment for OP in a patient with atypical chronic myeloid leukemia. Physicians should pay close attention to these complications in patients with hematologic malignancies.

Pleuritis associated with primary Sjogren syndrome.

We herein present a case of a 71-year-old woman with primary Sjogren's syndrome (SjS), who developed bilateral pleural effusion and ground glass opacity during treatment with low-dose prednisolone. The pleural effusion and bronchoalveolar lavage fluid revealed elevation of lymphocytes. Thoracoscopic pleural biopsy showed infiltration of lymphocytes with no evidence of other diseases, confirming SjS-related pleuritis. Therefore, we initiated 20 mg prednisolone and pleural effusion was rapidly resolved. Our results indicate that SjS can be rarely complicated with pleuritis. In addition, thoracoscopic pleural biopsy and a rapid response to steroid treatment would be helpful for diagnosing SjS-related pleuritis.

Promising Effect of Crizotinib on Anaplastic Lymphoma Kinase (ALK)-Positive Non-Small Cell Lung Cancer in an Elderly Patient with a Poor Performance Status: A Case Report and Literature Review.

Crizotinib is highly effective for anaplastic lymphoma kinase (ALK)-positive non-small cell lung cancer (NSCLC). However, it remains unclear whether crizotinib has a beneficial effect on elderly patients with ALK-positive NSCLC with a poor performance status (PS). We herein present the case of an 85-year-old man with stage IV ALK-positive NSCLC, whose PS score was 4 due to pericardial and pleural effusions. After initiating crizotinib therapy, a drastic response was observed and the PS score improved to 0. Adverse effects were manageable. Our results indicate that crizotinib could be an important choice when treating elderly patients with ALK-positive NSCLC with poor PS.

Clinical features of usual interstitial pneumonia with anti-neutrophil cytoplasmic antibody in comparison with idiopathic pulmonary fibrosis.

BACKGROUND AND OBJECTIVE: Myeloperoxidase anti-neutrophil cytoplasmic antibody (MPO-ANCA) is occasionally positive in patients with usual interstitial pneumonia (UIP). However, the differences from idiopathic pulmonary fibrosis (IPF/UIP) have not been well documented. We aimed to clarify the clinical, radiological and pathological features of UIP associated with MPO-ANCA (ANCA/UIP). METHODS: We retrospectively reviewed the medical records of 12 consecutive ANCA/UIP patients not manifesting microscopic polyangiitis and 108 IPF/UIP patients with no autoantibodies, both diagnosed by surgical lung biopsy. RESULTS: There was no significant difference in clinical background, laboratory results and pulmonary function tests between ANCA/UIP patients and IPF/UIP patients except for the percentage of bronchoalveolar lavage neutrophils. HRCT showed subpleural reticulation in both groups. Increased attenuation around honeycombing and cysts was significantly observed in ANCA/UIP. Pathologically, ANCA/UIP had more prominent inflammatory cell infiltration, lymphoid follicles with germinal centres and cellular bronchiolitis. During the disease course, three of 12 patients (25%) developed microscopic polyangiitis. Immunosuppressive treatment tended to be more effective in ANCA/UIP patients, and the survival time in ANCA/UIP patients tended to be longer than those with IPF/UIP. CONCLUSION: ANCA/UIP may be distinguishable from IPF/UIP with a combination of HRCT findings of increased attenuation around honeycombing and cysts and some of the characteristic pathological findings. In contrast to IPF/UIP, immunosuppressive treatment could be a therapeutic option for ANCA/UIP.

[Clinical characteristics of pulmonary Mycobacterium avium complex infection complicated with lung cancer].

OBJECTIVES: The coexistence of lung cancer and pulmonary Mycobacterium avium complex (MAC) infection has not been well reported. This study illustrated the clinical characteristics of pulmonary MAC infections complicated with lung cancer. PATIENTS AND METHODS: We conducted a retrospective analysis of the clinical characteristics of patients with pulmonary MAC infections complicated with newly diagnosed lung cancer between 2006 and 2012. RESULTS: Of 530 patients with pulmonary MAC infections, 13 (2.4%) were complicated with lung cancer. Six men and 7 women with a mean age of 73 years were also diagnosed with cancer, and 5 had a smoking history. Six patients were diagnosed concurrently, and 7 patients were diagnosed with pulmonary MAC infections prior to being diagnosed with cancer. Histological examination revealed adenocarcinoma, small cell carcinoma, and other cancer types in 9, 2, and 2 patients, respectively. Eleven of 13 patients had cancers of stages I-IIIA, and 10 underwent cancer resection. Analysis of the anatomical relationship between lung cancer and MAC revealed that both diseases were present in the same lobe in 10 patients. The disease extent was within one-third of a single lung field in 9 patients. Anti-MAC treatment was initiated in 7 patients, but was discontinued in 2 patients owing to side effects. Six patients did not receive anti-MAC treatment. CONCLUSION: In this study, lung cancer was frequent among patients with pulmonary MAC infections, and both diseases tended to be in the early stages. Physicians should consider coexisting lung cancer when managing MAC infections.

Neurally mediated syncope associated with small cell lung cancer: a case report and review.

We encountered a case of limited-disease small cell lung cancer with episodic syncope. The frequency of the syncopal attacks increased with the increase in the tumor size, thus a relationship was suspected to exist between the SCLC and syncope. Syncope was evaluated by history taking, 24-hour ECG monitoring, and coronary angiography. As orthostatic hypotension and cardiac disease could be excluded, we finally diagnosed this case as neurally mediated syncope. Serum tests for anti-Hu and anti-Yo antibodies were negative. A temporary pacemaker was inserted for sick sinus syndrome. This patient showed good response to the chemotherapy. No further syncopal attacks were observed after the second course of chemotherapy. Here, in addition we review four cases of SCLC with episodic syncope. Interestingly, in all cases, the tumor was located in the left hilum in close vicinity of the afferent vagal nerve (C-fibers) and mechano-receptor. Therefore, we thought that the mechanism underlying the syncope was mechano-receptor hypersensitivity.