SM3DD with segmented PCA: a comprehensive method for interpreting 3D spatial transcriptomics.

We developed Standardised Minimum 3D Distance (SM3DD), an entirely cell segmentation/annotation-free approach to the analysis of spatial RNA datasets, using it to compare lung tissue from 16 clinically normal individuals to those of 18 SARS-CoV-2 patients who died from acute respiratory distress syndrome. RNA spatial coordinates were determined using the CosMx™ Spatial Molecular Imager (Bruker Spatial Biology, US). For each individual transcript location, we calculated the three-dimensional distances to the nearest transcript of each transcript type, standardising the distances to each transcript type. Mean SM3DDs were compared between normal and SARS-CoV-2 patients. Notably, hierarchical clustering of the directional log10(P) values organized genes by functionality, making it easier to interpret biological contexts and for FKBP11, where a decrease in distance to MZT2A was the most significant difference, suggesting a role in interferon signaling. Using a segmented principal components analysis of the entire SM3DD dataset, we identified multiple pathways, including ‘SARS-CoV-2 infection’, even though the assay did not include any SARS-CoV-2 transcripts.

The role of corticosteroids in acute respiratory distress syndrome (ARDS) remains contentious. This study aims to investigate the prognostic significance of immune deficiency in patients with ARDS and its response to varying doses of corticosteroids. This single-center, retrospective cohort study enrolled 657 ARDS patients from January 24, 2008, to September 12, 2022, at Zhongshan Hospital of Fudan University, Shanghai, China. The patients were categorized into a discovery dataset (n=357) and a validation dataset (n=300), based on admission date. Further validation of the results in the validation dataset was used to enhance the credibility of the study conclusions. The study examined the association between immune deficiency and the patients' clinical characteristics, treatment measures, and prognosis. The primary outcome was 28-day mortality post disease onset. Data analysis was conducted from June 15, 2023 to August 15, 2023. The initial risk factor analysis in the discovery dataset was primarily based on the clinical characteristics, and the results suggested that immune deficiency likely impacted overall survival among patients receiving different doses of corticosteroid treatment. Multivariate analysis identified immune deficiency as an independent prognostic factor for overall survival in both the discovery and validation datasets. The final analysis revealed that patients with mild to moderate ARDS [discovery dataset: hazard ratio (HR) =1.719; 95% confidence interval (CI): 1.229-2.406; log-rank test P=0.001; validation dataset: HR =1.874; 95% CI: 1.238-2.837; log-rank test P=0.002] or severe ARDS (discovery dataset: HR =1.874; 95% CI: 1.007-3.488; log-rank test P=0.04; validation dataset: HR =1.698; 95% CI: 1.042-2.768; log-rank test P=0.03) with immune deficiency exhibited lower overall survival rates. Patients with mild to moderate ARDS and immune deficiency showed greater benefits from low-dose corticosteroid treatment (HR =0.409; 95% CI: 0.249-0.671; P<0.001 for interaction), whereas those with severe ARDS and immune deficiency benefitted from both low and high-dose treatments (low corticosteroid: HR =0.299; 95% CI: 0.136-0.654; high corticosteroid: HR =0.458; 95% CI: 0.214-0.981; P=0.005 for interaction). Immune deficiency is an independent risk factor in ARDS. Incorporating it into the disease severity grading system based on the Berlin criteria may enhance personalized treatment approaches for ARDS patients. These findings warrant further validation through prospective, large-scale, multicenter randomized controlled trials (RCTs).

The concern of today's communities is to find a way to prevent or treat COVID-19 and reduce its symptoms in the patients. However, the genetic mutations and more resistant strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerge; the designed vaccines and adjuvant therapies would potentially control the symptoms and severity of COVID-19. The most important complication of this viral infection is acute respiratory distress syndrome, which occurs due to the infiltration of leukocytes into the alveoli and the raised cytokine storm. Interferons, as a cytokine family in the host, play an important role in the immune-related antiviral defense and have been considered in the treatment protocols of COVID-19. In addition, it has been indicated that some nutrients, including vitamin D, magnesium and zinc are essential in the modulation of the immune system and interferon (IFN) signaling pathway. Several recent studies have investigated the treatment effect of vitamin D on COVID-19 and reported the association between optimal levels of this vitamin and reduced disease risk. In the present study, the synergistic action of vitamin D, magnesium and zinc in IFN signaling is discussed as a treatment option for COVID-19 involvement.

Acute respiratory distress syndrome (ARDS) is a life‐threatening form of acute lung injury and respiratory failure. The pandemic of SARS‐CoV‐2 has resulted in over 5 million deaths worldwide and many of those deaths have been attributed to complications associated with ARDS. No efficient pharmacological treatments for ARDS are currently available. In addition to lung injury and pulmonary inflammation, patients with ARDS have increased systemic inflammation. Previous insights have highlighted the role of cholinergic signalling in the vagus nerve‐based inflammatory reflex in controlling inflammation (Annu Rev Immunol, 2018, 36:783). Cholinergic anti‐inflammatory signalling can be activated by galantamine ‐ a centrally acting acetylcholinesterase inhibitor that is also clinically approved (for the treatment of Alzheimer’s disease). Here we examined the efficacy of galantamine in attenuating ARDS severity and inflammation in mice. We used a recently developed model of direct acute lung injury and ARDS, in which intratracheal (i.t.) hydrochloric acid (0.1N HCl, 2ml/kg) instillation is combined with LPS (10 mg/kg, i.t.) instillation 24h later in anesthetized mice. Male, 12‐week‐old C57BL/6 mice (n=7‐9), were subjected to this two hit ARDS model and treated 30 mins prior to each insult with galantamine (4 mg/kg, i.p.) or vehicle. Mice were euthanized 6h after LPS instillation and blood and bronchoalveolar lavage (BAL) fluid were collected. Galantamine significantly lowered the levels of BAL myeloperoxidase – an indicator of the accumulation of activated neutrophils in the airspaces of the lung (p = 0.0021) and the BAL total protein ‐ an indicator of alveolar permeability (p = 0.0076), compared with vehicle‐treated mice. BAL pro‐inflammatory cytokine levels were also reduced by galantamine, compared with vehicle‐treated mice – TNF (p = 0.0274), IL‐6 (p = 0.0009), and IL‐1β (p = 0.0380). In addition, treatment with galantamine significantly lowered the levels of serum pro‐inflammatory cytokines ‐ TNF (p = 0.0015), IL‐6 (p = 0.0089), and IL‐1β (p = 0.0149). In conclusion, galantamine reduced the severity of ARDS in mice and alleviated the local and systemic inflammatory responses. These results are of interest for further preclinical and clinical development of galantamine in the treatment of ARDS.

ABSTRACTIntroduction: Acute respiratory distress syndrome (ARDS) is a heterogeneous and multifactorial disease; it is a common and devastating condition that has a high mortality. Treatment is limited to supportive measures hence novel pharmacological approaches are necessary. We propose a new direction in ARDS research; this means moving away from thinking about individual inflammatory mediators and instead investigating how packaged information is transmitted between cells. Microvesicles (MVs) represent a novel vehicle for inter-cellular communication with an emerging role in ARDS pathophysiology.Areas covered: This review examines current approaches to ARDS and emerging MV research. We describe advances in our understanding of microvesicles and focus on their pro-inflammatory roles in airway and endothelial signaling. We also offer reasons for why MVs are attractive therapeutic targets.Expert opinion: MVs have a key role in ARDS pathophysiology. Preclinical studies must move away from simple models toward more realistic scenarios while clinical studies must embrace patient heterogeneity. Microvesicles have the potential to aid identification of patients who may benefit from particular treatments and act as biomarkers of cellular status and disease progression. Understanding microvesicle cargoes and their cellular interactions will undoubtedly uncover new targets for ARDS.

Decision letter: Single-cell transcriptomic atlas of lung microvascular regeneration after targeted endothelial cell ablation

The coronavirus disease 2019 (COVID-19) pandemic constitutes a global health emergency. Currently, there are no completely effective therapeutic medications for the management of this outbreak. The cytokine storm is a hyperinflammatory medical condition due to excessive and uncontrolled release of pro-inflammatory cytokines in patients suffering from severe COVID-19, leading to the development of acute respiratory distress syndrome (ARDS) and multiple organ dysfunction syndrome (MODS) and even mortality. Understanding the pathophysiology of COVID-19 can be helpful for the treatment of patients. Evidence suggests that the levels of tumor necrosis factor alpha (TNF-α) and interleukin (IL)-1 and IL-6 are dramatically different between mild and severe patients, so they may be important contributors to the cytokine storm. Several serum markers can be predictors for the cytokine storm. This review discusses the cytokines involved in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, focusing on interferons (IFNs) and ILs, and whether they can be used in COVID-19 treatment. Moreover, we highlight several microRNAs that are involved in these cytokines and their role in the cytokine storm caused by COVID-19.

The goal of this study is to reveal the hub genes and molecular mechanisms of the coronavirus disease 2019 (COVID‐19) acute respiratory distress syndrome (ARDS) based on the genome‐wide RNA sequencing dataset. The RNA sequencing dataset of COVID‐19 ARDS was obtained from GSE163426. A total of 270 differentially expressed genes (DEGs) were identified between COVID‐19 ARDS and control group patients. Functional enrichment analysis of DEGs suggests that these DEGs may be involved in the following biological processes: response to cytokine, G‐protein coupled receptor activity, ionotropic glutamate receptor signalling pathway and G‐protein coupled receptor signalling pathway. By using the weighted correlation network analysis approach to analyse these DEGs, 10 hub DEGs that may play an important role in COVID‐19 ARDS were identified. A total of 67 potential COVID‐19 ARDS targetted drugs were identified by a complement map analysis. Immune cell infiltration analysis revealed that the levels of T cells CD4 naive, T cells follicular helper, macrophages M1 and eosinophils in COVID‐19 ARDS patients were significantly different from those in control group patients. In conclusion, this study identified 10 COVID‐19 ARDS‐related hub DEGs and numerous potential molecular mechanisms through a comprehensive analysis of the RNA sequencing dataset and also revealed the difference in immune cell infiltration of COVID‐19 ARDS.

Although critical for host defense, innate immune cells are also pathologic drivers of acute respiratory distress syndrome (ARDS). Innate immune dynamics during Coronavirus Disease 2019 (COVID-19) ARDS, compared to ARDS from other respiratory pathogens, is unclear. Moreover, mechanisms underlying the beneficial effects of dexamethasone during severe COVID-19 remain elusive. Using single-cell RNA sequencing and plasma proteomics, we discovered that, compared to bacterial ARDS, COVID-19 was associated with expansion of distinct neutrophil states characterized by interferon (IFN) and prostaglandin signaling. Dexamethasone during severe COVID-19 affected circulating neutrophils, altered IFNactive neutrophils, downregulated interferon-stimulated genes and activated IL-1R2+ neutrophils. Dexamethasone also expanded immunosuppressive immature neutrophils and remodeled cellular interactions by changing neutrophils from information receivers into information providers. Male patients had higher proportions of IFNactive neutrophils and preferential steroid-induced immature neutrophil expansion, potentially affecting outcomes. Our single-cell atlas (see ‘Data availability’ section) defines COVID-19-enriched neutrophil states and molecular mechanisms of dexamethasone action to develop targeted immunotherapies for severe COVID-19.

Hypoxemia is a defining feature of acute respiratory distress syndrome (ARDS), an often-fatal complication of pulmonary or systemic inflammation, yet the resulting tissue hypoxia, and its impact on immune responses, is often neglected. In the present study, we have shown that ARDS patients were hypoxemic and monocytopenic within the first 48 h of ventilation. Monocytopenia was also observed in mouse models of hypoxic acute lung injury, in which hypoxemia drove the suppression of type I interferon signaling in the bone marrow. This impaired monopoiesis resulted in reduced accumulation of monocyte-derived macrophages and enhanced neutrophil-mediated inflammation in the lung. Administration of colony-stimulating factor 1 in mice with hypoxic lung injury rescued the monocytopenia, altered the phenotype of circulating monocytes, increased monocyte-derived macrophages in the lung and limited injury. Thus, tissue hypoxia altered the dynamics of the immune response to the detriment of the host and interventions to address the aberrant response offer new therapeutic strategies for ARDS.

Acute respiratory distress syndrome (ARDS)/Acute lung injury (ALI), characterized by severe hypoxemia and pulmonary edema, involves mitochondrial dysfunction. Cytidine/uridine monophosphate kinase 2 (Cmpk2), a mitochondrial metabolic enzyme, modulates inflammation and senescence, yet its role in ARDS remains unclear. We investigated Cmpk2's function inPseudomonas aeruginosa (P. aeruginosa)-induced ALI using Cmpk2 global knockout (KO) mice. Cmpk2 was identified through mitochondrial gene expression analysis of ARDS datasets (GEO). Murine ALI was induced by intratrachealP. aeruginosa injection. Lung pathology (hematoxylin and eosin staining), leukocyte recruitment (flow cytometry), and cytokines (ELISA) were assessed.GO/KEGG analyses were conducted to identify Cmpk2-associated biological processes and pathways. The expression of Cmpk2 in leukocyte populations was analyzed using single-cell RNA sequencing (scRNA-seq) data from ARDS patient samples. Mouse neutrophils' phagocytosis of P. aeruginosa was quantified by flow cytometry. Zebrafish embryos were infected withP. aeruginosaandStaphylococcus aureusfor bacterial burden and survival assays. Cmpk2 expression was significantly upregulated in ARDS. Cmpk2 KO exacerbated P. aeruginosa-induced ALI in mice, as evidenced by increased pathological damage and permeability, elevated proinflammatory cytokines and enhanced neutrophil infiltration. GO/KEGG analyses linked Cmpk2 to innate immunity. scRNA-seq analysis revealed an enriched expression of Cmpk2 in neutrophils. Cmpk2 deficiency impaired neutrophil phagocytosis and reduced host survival during bacterial infection, accomplished by decreased STING expression. The differences in phagocytosis between the wild-type and Cmpk2 KO mouse neutrophils/zebrafish embryos were eliminated by STING inhibitor C176. Cmpk2 protects against pneumonia by attenuating neutrophil recruitment and enhancing bacterial phagocytosis via STNG-dependent mechanisms.

The remote sensing hyperspectral images (HSIs) usually comprise many important information of the land covers capturing through a set of hundreds of narrow and contiguous spectral wavelength bands. Appropriate classification performance can only offer the required knowledge from these immense bands of HSI since the classification result is not reasonable using all the original features (bands) of the HSI. Although it is not easy to calculate the intrinsic features from the bands, band (dimensionality) reduction techniques through feature extraction and feature selection are usually applied to increase the classification result and to fix the curse of dimensionality problem. Though the Principal Component Analysis (PCA) has been commonly adopted for the feature reduction of HSI, it can often fail to extract the local useful characteristics of the HSI for effective classification as it considers the global statistics of the HSI. Consequently, Segmented-PCA (SPCA), Spectrally-Segmented-PCA (SSPCA), Folded-PCA (FPCA) and Superpixelwise PCA (SuperPCA) have been introduced for better feature extraction of HSI in diverse ways. In this paper, feature extraction through SPCA & FPCA and SSPCA & FPCA, termed as Segmented-FPCA (SFPCA) and Spectrally-Segmented-FPCA (SSFPCA) respectively, has further been improved through applying FPCA on the highly correlated or spectrally separated bands’ segments of the HSI rather than not applying the FPCA on the entire dataset directly. The proposed methods are compared and analysed for a real mixed agricultural and an urban HSI classification using per-pixel SVM classifier. The experimental result shows that the classification performance using SSFPCA and SFPCA outperforms that of using conventional PCA, SPCA, SSPCA, FPCA, SuperPCA and using the entire original dataset without employing any feature reduction. Moreover, the proposed feature extraction methods provide the least memory and computation cost complexity.

Background: Capsaicin is commonly used as a flavoring and a riot control agent. However, long-term exposure or high doses can cause acute lung injury in military and police personnel. The mechanisms underlying capsaicin-induced pulmonary toxicity remain unclear. Therefore, this study investigated the molecular mechanisms involved in capsaicin-induced acute lung injury using C57BL/6N mice. Methods: Through both transcriptomic and proteomic analyses of mouse lung tissue, we identified the involvement of the TNF signaling pathway in capsaicin-mediated acute lung injury. Next, we explored the role of TNF signaling in the progression of acute lung injury to identify potential therapeutic targets. In a capsaicin-induced acute lung injury mouse model and A549 cells, we assessed the therapeutic potential of the TNF-α antibody Nerelimomab. Compared with the control group, TNF-α up-regulation was observed, which correlated with increased pathological changes and elevated IL-6 (p < 0.01) and IL-18 (p < 0.01) levels, both in vivo and in vitro. Results: Flow cytometry revealed that compared to the capsaicin group, Nerelimomab treatment reduced the number of capsaicin-induced apoptotic cells (p < 0.001) and was associated with an increased Bcl-2/Bax ratio (p < 0.01) and reduced cleaved caspase 3 expression (p < 0.001). Analysis of A549 cells treated with capsaicin and Nerelimomab corroborated these results. These findings confirm the involvement of the TNF signaling pathway in capsaicin-induced acute lung injury and the apoptosis of alveolar epithelial cells. Conclusions: In conclusion, capsaicin inhalation can cause acute lung injury, and targeting the TNF signaling pathway offers a promising therapeutic strategy. Nerelimomab demonstrates significant potential in alleviating acute lung injury by inhibiting inflammatory mediator release and diminishing apoptosis. Based on transcriptomic and proteomic analyses, this study highlights the crucial role of the TNF signaling pathway in capsaicin-induced acute lung injury and supports the therapeutic efficacy of Nerelimomab in reducing epithelial apoptosis.

Objective To investigate the role of p38 mitogan-activated protein kinase signal transduction pathway in lipopolysaccha-ricle-indaced acute lung injury (ALI) in rats. Methods 48 wistar rats were randomly divided into 3 groups, saline control group (group A), lipopolysaccharide (LPS) group(group B) and SB203580 group(group C). Models of lipepelysaccharide-imluced ALI were used to oh-serve the expression of p38MAPK in rat lung, protein content, the ratio of neutrophiles in bronchoalveolar lavage fluid (BALF) , pulmonary MDA content and the activities of serum NO. After LPS dripping for 6 hours, arterial blood was drawn for analysis and lung tissue was detec-ted. Results Compared with those in group A, expression of p38MAPK were markedly increased in group B and C (P<0.01). But in group C, expression of P38MAPK was significantly lower than that in group B (P<0.05). The protein content, the ratio of neutrophiles in bronchoalveolar lavage fluid (BALF), content of pulmonary MDA and the activities of serum NO in group B, C were significantly higher than those in group A (P<0.01). There was a significant decrease in the level of arterial bicarbonate and partial pressure of oxygen in group B and C (P<0.01). Compared with those in group B, these indexes of lung injury were significantly lower while the level of arterial bicar-bonate and partial pressure of oxygen was increased in group C(P <0. 05 orP <0. 01). Under light microscope, the pathologic changes in-duced by LPS were significantly attenuated by SB2035g0. Conclusion The activation of P38MAPK play an important role in the mechanism of lipopolysaccharide-induced ALI. Key words: p38 mitogen-aetivated protein kinases; Respiratory distress syndrome, adult; Endotoxins

Better prognostic predictors for invasive candidiasis (IC) are needed to tailor and individualize therapeutic decision-making and minimize its high morbidity and mortality. We investigated whether molecular profiling of IgG-antibody response to the whole soluble Candida proteome could reveal a prognostic signature that may serve to devise a clinical-outcome prediction model for IC and contribute to known IC prognostic factors. By serological proteome analysis and data-mining procedures, serum 31-IgG antibody-reactivity patterns were examined in 45 IC patients randomly split into training and test sets. Within the training cohort, unsupervised two-way hierarchical clustering and principal-component analyses segregated IC patients into two antibody-reactivity subgroups with distinct prognoses that were unbiased by traditional IC prognostic factors and other patients-related variables. Supervised discriminant analysis with leave-one-out cross-validation identified a five-IgG antibody-reactivity signature as the most simplified and accurate IC clinical-outcome predictor, from which an IC prognosis score (ICPS) was derived. Its robustness was confirmed in the test set. Multivariate logistic-regression and receiver-operating-characteristic curve analyses demonstrated that the ICPS was able to accurately discriminate IC patients at high risk for death from those at low risk and outperformed conventional IC prognostic factors. Further validation of the five-IgG antibody-reactivity signature on a multiplexed immunoassay supported the serological proteome analysis results. The five IgG antibodies incorporated in the ICPS made biologic sense and were associated either with good-prognosis and protective patterns (those to Met6p, Hsp90p, and Pgk1p, putative Candida virulence factors and antiapoptotic mediators) or with poor-prognosis and risk patterns (those to Ssb1p and Gap1p/Tdh3p, potential Candida proapoptotic mediators). We conclude that the ICPS, with additional refinement in future larger prospective cohorts, could be applicable to reliably predict patient clinical-outcome for individualized therapy of IC. Our data further provide insights into molecular mechanisms that may influence clinical outcome in IC and uncover potential targets for vaccine design and immunotherapy against IC.