Selection of AECOPD-specific immunomodulatory biomarkers by integrating genomics and proteomics with clinical informatics

Use of the Serum Level of Cholinesterase as a Prognostic Marker of Nonfatal Clinical Outcomes in Patients Hospitalized with Acute Exacerbations of Chronic Obstructive Pulmonary Disease

Introduction

Acute exacerbation of chronic obstructive pulmonary disease (AECOPD) contributes to a poor prognosis. Reliable biomarkers to predict adverse outcomes during hospitalization are important.

Aim

To investigate the relationship between the serum cholinesterase (ChE) level and adverse clinical outcomes, including hypoxemia severity, hypercapnia, duration of hospital stay (DoHS), and noninvasive ventilation (NIV) requirement, in patients with AECOPD.

Methods

Patients hospitalized with AECOPD in the Wuhu Hospital of Traditional Chinese Medicine between January 2017 and December 2021 were included.

Results

A total of 429 patients were enrolled. The serum ChE level was significantly lower in patients with hypercapnia, who required NIV during hospitalization and who had a DoHS of >10 days, with an oxygenation index < 300. The ChE level was correlated negatively with the C-reactive protein level and neutrophil-to-lymphocyte ratio and correlated positively with the serum albumin level. Multivariate logistic regression analysis indicated that a serum ChE level of ≤4116 U/L (OR = 2.857, 95% CI = 1.46-5.58, p = 0.002) was associated significantly with NIV requirement.

Conclusions

The serum ChE level was correlated significantly with complicating severe hypoxemia, hypercapnia, prolonged DoHS, and the need for NIV in patients hospitalized with AECOPD. The serum ChE level is a clinically important risk-stratification biomarker in patients hospitalized with AECOPD.

COPD: systemic proteomic profiles in frequent and infrequent exacerbators

Background

Some patients with COPD suffer frequent exacerbations (FE). We hypothesised that their systemic proteomic profile would be different from that of non-frequent exacerbators (NFE). The objective of the present study was to contrast the systemic proteomic profile in FE versus NFE. As a reference, we also determined the systemic proteomic profile of healthy controls (HC) and COPD patients during an actual episode of exacerbation (AE).

Methods

In the analysis we included 40 clinically stable COPD patients (20 FE and 20 NFE), and 20 HC and 10 AE patients. Their plasma samples were analysed by combining two complementary proteomic approaches: label-free liquid chromatography-tandem mass spectrometry and multiplex immunoassays. Gene Ontology annotation, pathway enrichment and network analyses were used to investigate molecular pathways associated with differentially abundant proteins/peptides (DAPs).

Results

Compared with HC, we identified 40 DAPs in FE, 10 in NFE and 63 in AE. Also compared to HC, pathway functional and protein-protein network analyses revealed dysregulation of inflammatory responses involving innate and antibody-mediated immunity in COPD, particularly in the FE group, as well as during an AE episode. Besides, we only identified alterations in the complement and coagulation cascades in AE.

Conclusion

There are specific plasma proteome profiles associated with FE, which are partially shared with findings observed during AE, albeit others are uniquely present during the actual episode of AE.

Biomarkers of chronic airflow limitation and COPD identified by mass spectrometry

Rationale

COPD affects 300 million people worldwide and is the third leading cause of death according to World Health Organization global health estimates. Early symptoms are subtle, and so COPD is often diagnosed at an advanced stage. Thus, there is an unmet need for biomarkers that can identify individuals at early stages of the disease before clinical symptoms have manifested. To date, few biomarkers are available for clinical diagnostic use in COPD.

Methods

We evaluated a panel of serum biomarkers related to inflammation and infection for their ability to discriminate between 77 subjects with chronic airflow limitation (CAL) and 142 subjects with COPD, versus 150 healthy subjects (divided into two control groups that were matched with regards to age, gender and smoking to CAL and COPD). Healthy subjects and CAL were from Burden of Obstructive Lung Disease (BOLD), a population-based study. CAL was defined by post-bronchodilatory forced expiratory volume in 1 s/forced vital capacity ratio <0.7 in the BOLD population. COPD subjects were from Tools for Identifying Exacerbations (TIE), a COPD patient cohort. Quantification of 100 biomarker candidates was done by liquid chromatography-tandem mass spectrometry.

Results

Several protein-derived peptides were upregulated in CAL, compared to controls; most notably peptides representing histidine-rich glycoprotein (HRG), α1-acid glycoprotein (AGP1), α1-antitrypsin (α1AT) and fibronectin. Out of these, HRG-, AGP1- and α1AT-specific peptides were also elevated in the COPD cohort.

Conclusion

HRG, AGP1 and α1AT biomarkers distinguish subjects with CAL and COPD from healthy controls. HRG and AGP1 represent novel findings.

Regulatory roles of Osteopontin in lung epithelial inflammation and epithelial-telocyte interaction

BACKGROUND

Lung epithelial cells play important roles in lung inflammation and injury, although mechanisms remain unclear. Osteopontin (OPN) has essential roles in epithelial damage and repair and in lung cancer biological behaviours. Telocyte (TC) is a type of interstitial cell that interacts with epithelial cells to alleviate acute inflammation and lung injury. The present studies aim at exploring potential mechanisms by which OPN regulates the epithelial origin lung inflammation and the interaction of epithelial cells with TCs in acute and chronic lung injury.

METHODS

The lung disease specificity of OPN and epithelial inflammation were defined by bioinformatics. We evaluated the regulatory roles of OPN in OPN-knockdown or over-expressed bronchial epithelia (HBEs) challenged with cigarette smoke extracts (CSE) or in animals with genome OPN knockout (gKO) or lung conditional OPN knockout (cKO). Acute lung injury and chronic obstructive pulmonary disease (COPD) were induced by smoking or lipopolysaccharide (LPS). Effects of OPN on PI3K subunits and ERK were assessed using the inhibitors. Spatialization and distribution of OPN, OPN-positive epithelial subtypes, and TCs were defined by spatial transcriptomics. The interaction between HBEs and TCs was assayed by the co-culture system.

RESULTS

Levels of OPN expression increased in smokers, smokers with COPD, and smokers with COPD and lung cancer, as compared with healthy nonsmokers. LPS and/or CSE induced over-production of cytokines from HBEs, dependent upon the dysfunction of OPN. The severity of lung inflammation and injury was significantly lower in OPN-gKO or OPN-cKO mice. HBEs transferred with OPN enhanced the expression of phosphoinositide 3-kinase (PI3K)CA/p110α, PIK3CB/p110β, PIK3CD/p110δ, PIK3CG/p110γ, PIK3R1, PIK3R2 or PIK3R3. Spatial locations of OPN and OPN-positive epithelial subtypes showed the tight contact of airway epithelia and TCs. Epithelial OPN regulated the epithelial communication with TCs, and the down-regulation of OPN induced more alterations in transcriptomic profiles than the up-regulation.

CONCLUSION

Our data evidenced that OPN regulated lung epithelial inflammation, injury, and cell communication between epithelium and TCs in acute and chronic lung injury. The conditional control of lung epithelial OPN may be an alternative for preventing and treating epithelial-origin lung inflammation and injury.

Major depressive disorder plays a vital role in the pathway from gastroesophageal reflux disease to chronic obstructive pulmonary disease: a Mendelian randomization study

Background: Observational studies have shown a bidirectional association between chronic obstructive pulmonary disease (COPD) and gastroesophageal reflux disease (GERD), but it is not clear whether this association is causal. In our previous study, we found that depression was a hot topic of research in the association between COPD and GERD. Is major depressive disorder (MDD) a mediator of the association between COPD and GERD? Here, we evaluated the causal association between COPD, MDD, and GERD using Mendelian randomization (MR) study. Methods: Based on the FinnGen, United Kingdom Biobank, and Psychiatric Genomics Consortium (PGC) databases, we obtained genome-wide association study (GWAS) summary statistics for the three phenotypes from 315,123 European participants (22,867 GERD cases and 292,256 controls), 462,933 European participants (1,605 COPD cases and 461,328 controls), and 173,005 European participants (59,851 MDD cases and 113,154 controls), respectively. To obtain more instrumental variables to reduce bias, we extracted relevant single-nucleotide polymorphisms (SNPs) for the three phenotypes from published meta-analysis studies. Bidirectional MR and expression quantitative trait loci (eQTL)-MR were performed using the inverse variance weighting method to assess the causal association between GERD, MDD, and COPD. Results: There was no evidence of a causal effect between GERD and COPD in the bidirectional MR analysis [forward MR for GERD on COPD: odds ratios (OR) = 1.001, p = 0.270; reverse MR for COPD on GERD: OR = 1.021, p = 0.303]. The causal effect between GERD and MDD appeared to be bidirectional (forward MR for GERD on MDD: OR = 1.309, p = 0.006; reverse MR for MDD on GERD: OR = 1.530, p < 0.001), while the causal effect between MDD and COPD was unidirectional (forward MR for MDD on COPD: OR = 1.004, p < 0.001; reverse MR for COPD on MDD: OR = 1.002, p = 0.925). MDD mediated the effect of GERD on COPD in a unidirectional manner (OR = 1.001). The results of the eQTL-MR were consistent with those of the bidirectional MR. Conclusion: MDD appears to play a vital role in the effect of GERD on COPD. However, we have no evidence of a direct causal association between GERD and COPD. There is a bidirectional causal association between MDD and GERD, which may accelerate the progression from GERD to COPD.

Novel lipidomes profile and clinical phenotype identified in pneumoconiosis patients

BACKGROUND

Pneumoconiosis is a group of occupational lung diseases caused by the inhalation of mineral dust in the lungs, leading to lung dysfunction. Patients with pneumoconiosis are usually accompanied by weight loss, which suggests a lipid metabolism disorder. Recent progress in lipidomics uncovered detailed lipid profiles that play important roles in respiratory diseases, such as asthma, lung cancer and lung injury. The purpose of this study was to shed light on the different expression of lipidome between pneumoconiosis and healthy, hoping to bring new ideas for the diagnosis and treatment of pneumoconiosis.

METHODOLOGY

This non-matching case-control study was performed among 96 subjects (48 outpatients with male pneumoconiosis and 48 healthy volunteers), data of clinical phenotypes were recorded, and plasma biochemistry (lipidomic profiles) was tested for both pneumoconiosis patients and healthy controls. A total of 426 species in 11 lipid classes were analyzed by high-performance liquid chromatography coupled with triple quadrupole tandem mass spectrometry (HPLC-QqQ-MS) for the cases and controls. We also analyzed the correlation of lipid profiles with clinical phenomes from pneumoconiosis patients by expression quantitative trait locus (eQTL) model to evaluate trans-nodules between lipidomic profiles and clinical phenomes. All visually re-checked data were analyzed using appropriate statistical tools (t-test or one-way ANOVA test) on SPSS.

RESULTS

Compared with healthy people, 26 significantly increased (> 1.5-fold) and 30 decreased lipid elements (< 2/threefold) in patients with pneumoconiosis were identified (P values all < 0.05). The majority of those elevated lipid elements were phosphatidylethanolamines (PEs), and the minority were free fatty acids (FFAs), while phosphatidylcholines (PCs) and lysophosphatidylcholines (lysoPCs) declined in pneumoconiosis. Clinical trans-omics analyses demonstrated that phenomes in pneumoconiosis connections with multiple lipids, which showed that pH, lung function, mediastinal lymph node calcification, and complication were highly correlated with lipid elements. Furthermore, up-regulated PE was corresponded to pH, smoking history and mediastinal lymph node calcification. PC was corresponded to dust exposure history, BMI and mediastinal lymph node calcification.

CONCLUSION

We found altered lipid panels between male pneumoconiosis patients and healthy people by qualitatively and quantitatively measured plasma lipidomic profiles. The trans-omic analysis between clinical phenomes and lipidomes might have the potential to uncover the heterogeneity of lipid metabolism of pneumoconiosis patients and to screen out clinically significant phenome-based lipid panels.

cAMP-PDE signaling in COPD: Review of cellular, molecular and clinical features

Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death among non-contagious diseases in the world. PDE inhibitors are among current medicines prescribed for COPD treatment of which, PDE-4 family is the predominant PDE isoform involved in hydrolyzing cyclic adenosine monophosphate (cAMP) that regulates the inflammatory responses in neutrophils, lymphocytes, macrophages and epithelial cells The aim of this study is to investigate the cellular and molecular mechanisms of cAMP-PDE signaling, as an important pathway in the treatment management of patients with COPD. In this review, a comprehensive literature review was performed about the effect of PDEs in COPD. Generally, PDEs are overexpressed in COPD patients, resulting in cAMP inactivation and decreased cAMP hydrolysis from AMP. At normal amounts, cAMP is one of the essential agents in regulating metabolism and suppressing inflammatory responses. Low amount of cAMP lead to activation of downstream inflammatory signaling pathways. PDE4 and PDE7 mRNA transcript levels were not altered in polymorphonuclear leukocytes and CD8 lymphocytes originating from the peripheral venous blood of stable COPD subjects compared to healthy controls. Therefore, cAMP-PDE signaling pathway is one of the most important signaling pathways involved in COPD. By examining the effects of different drugs in this signaling pathway critical steps can be taken in the treatment of this disease.

Predictive value of the hemoglobin-albumin-lymphocyte-platelet (HALP) index for ICU mortality in patients with acute exacerbations of chronic obstructive pulmonary disease (AECOPD)

The combined index of hemoglobin, albumin, lymphocyte, and platelet (HALP) is a novel indicator reflecting systemic inflammation and nutritional status. To explore the relationship between HALP score and ICU mortality risk in patients with acute exacerbations of chronic obstructive pulmonary disease (AECOPD). A total of 1533 AECOPD patients from the eICU Collaborative Research Database (eICU-CRD) between 2014 and 2015 were included in this retrospective cohort study. Univariate and multivariate Cox proportional hazards models were utilized to investigate the association of HALP score, platelet-to-lymphocyte ratio (PLR) score, and lymphocyte-to-monocyte ratio (LMR) score with the ICU mortality risk in patients with AECOPD. Stratified analyses were performed based on patients' ICU admission type, body mass index (BMI), and Acute Physiology, Age and Chronic Health Evaluation IV (APACHE IV) score. Of these 1533 AECOPD patients, 123 (8.00%) patients died in the ICU. Low HALP score [hazard ratio (HR) = 1.69; 95% confidence interval (CI) 1.14-2.53] and low LMR score (HR = 1.60; 95% CI 1.07-2.39) were associated with an increased ICU mortality risk in patients with AECOPD after adjusting for all confounders. Stratified analyses indicated that low HALP score were still associated with a higher ICU mortality risk in patients admitted to ICU by emergency (HR = 1.81; 95% CI 1.11-2.96), obese patients (HR = 2.81; 95% CI 1.29-6.10), and patients with low APACHE scores (HR = 2.87; 95% CI 1.75-4.69). Low HALP score was associated with an increased risk of ICU mortality in patients with AECOPD, suggesting that the HALP score may be a novel prognostic predictor in patients with AECOPD.

Comparison of CRP, Procalcitonin, Neutrophil Counts, Eosinophil Counts, sTREM-1, and OPN between Pneumonic and Nonpneumonic Exacerbations in COPD Patients

Introduction

The patients with community-acquired pneumonia (CAP) and acute exacerbations of COPD (AECOPD) could have a higher risk of acute and severe respiratory illness than those without CAP in AECOPD. Consequently, early identification of pneumonia in AECOPD is quite important. Methods. 52 subjects with AECOPD + CAP and 93 subjects with AECOPD from two clinical centers were enrolled in this prospective observational study. The values of osteopontin (OPN), soluble triggering receptor expressed on myeloid cells-1 (sTREM-1), C-reactive protein (CRP), procalcitonin (PCT), eosinophil (EOS) counts, and neutrophil (Neu) counts in blood on the first day of admission and clinical symptoms were compared in AECOPD and AECOPD + CAP. In addition, subgroup analyses of biomarker difference were conducted based on the current use of inhaled glucocorticoids (ICS) or systemic corticosteroids (SCS).

Results

Patients with AECOPD + CAP had increased sputum volume, sputum purulence, diabetes mellitus, and longer hospital stays than AECOPD patients (p < 0.05). A clinical logistic regression model showed among the common clinical symptoms, purulent sputum can independently predict pneumonia in AECOPD patients after adjusting for a history of diabetes. At day 1, AECOPD + CAP patients had higher values of Neu, CRP, PCT, and OPN, while serum sTREM-1 levels and EOS counts were similar in the two groups. CRP fared best at predicting AECOPD with CAP (p < 0.05 for the test of difference), while OPN had similar accuracy with Neu, PCT, and purulent sputum (p > 0.05 for the test of difference). Multivariate analysis, including clinical symptoms and biomarkers, suggested that CRP ≥15.8 mg/dL at day 1 was a only promising predictor of pneumonia in AECOPD. CRP and OPN were not affected by ICS or SCS.

Conclusions

CRP ≥15.8 mg/dL is an ideal promising predictor of pneumonia in AECOPD, and its plasma level is not affected by ICS or SCS. The diagnostic performance of CRP is not significantly improved when combined with clinical symptoms or other markers (OPN, PCT, and Neu).

A cellular census of human peripheral immune cells identifies novel cell states in lung diseases

Increasing evidence supports a central role of the immune system in lung diseases. Understanding how immunological alterations between lung diseases provide opportunities for immunotherapy. Exhausted T cells play a key role of immune suppression in lung cancer and chronic obstructive pulmonary disease was proved in our previous study. The present study aims to furthermore define molecular landscapes and heterogeneity of systemic immune cell target proteomic and transcriptomic profiles and interactions between circulating immune cells and lung residential cells in various lung diseases. We firstly measured target proteomic profiles of circulating immune cells from healthy volunteers and patients with stable pneumonia, stable asthma, acute asthma, acute exacerbation of chronic obstructive pulmonary disease, chronic obstructive pulmonary disease and lung cancer, using single-cell analysis by cytometry by time-of-flight with 42 antibodies. The nine immune cells landscape was mapped among those respiratory system diseases, including CD4+ T cells, CD8+ T cells, dendritic cells, B cells, eosinophil, γδT cells, monocytes, neutrophil and natural killer cells. The double-negative T cells and exhausted CD4+ central memory T cells subset were identified in patients with acute pneumonia. This T subset expressed higher levels of T-cell immunoglobulin and mucin domain-containing protein 3 (Tim3) and T-cell immunoreceptor with Ig and ITIM domains (TIGIT) in patients with acute pneumonia and stable pneumonia. Biological processes and pathways of immune cells including immune response activation, regulation of cell cycle and pathways in cancer in peripheral blood immune cells were defined by bulk RNA sequencing (RNA-seq). The heterogeneity among immune cells including CD4+ , CD8+ T cells and NK T cells by single immune cell RNA-seq with significant difference was found by single-cell sequencing. The effect of interstitial telocytes on the immune cell types and immune function was finally studied and the expressions of CD8a and chemokine C-C motif receptor 7 (CCR7) were increased significantly in co-cultured groups. Our data indicate that proteomic and transcriptomic profiles and heterogeneity of circulating immune cells provides new insights for understanding new molecular mechanisms of immune cell function, interaction and modulation as a source to identify and develop biomarkers and targets for lung diseases.

Oscillating dietary crude protein concentrations increase N retention of calves by affecting urea-N recycling and nitrogen metabolism of rumen bacteria and epithelium

The purpose of this study was to investigate the effects of oscillating crude protein (CP) concentration diet on the nitrogen utilization efficiency (NUE) of calves and determine its mechanism. Twelve Holstein calves were assigned randomly into static protein diet (SP, 149 g/kg CP) and oscillating protein diet (OP, 125 and 173 g/kg CP diets oscillated at 2-d intervals) groups. After 60 days of feeding, the weights of total stomach, rumen and omasum tended to increase in calves fed OP. The apparent crude fat digestibility, NUE and energy metabolism also increased. In terms of urea-N kinetics evaluated by urea-¹⁵N¹⁵N isotope labeling method, the urea-N production and that entry to gastrointestinal tended to increase, and urea-N reused for anabolism increased significantly in calves fed OP during the low protein phase. These data indicate that urea-N recycling contributed to improving NUE when dietary protein concentration was low. In addition, the differentially expressed genes in rumen epithelium and the rumen bacteria involved in protein and energy metabolism promoted the utilization of dietary protein in calves fed OP.

Multi-Omics study on biomarker and pathway discovery of chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) is a common heterogeneous respiratory disease characterized by persistent and incompletely reversible airflow limitation. Due to the heterogeneity and phenotypes complexity of COPD, traditionally diagnostic methods can only give limited information on predicted results and treatment, which are not sufficient for accurate diagnosis and evaluation. With the development of omics technologies in recent years, genomics, proteomics, and metabolomics are widely used in the study of COPD, providing good tools for discovering biomarkers to diagnose and elucidate the complex mechanism of COPD. In this review, we summarized the biomarkers of COPD based on metabolomic, proteomic and transcriptomic studies that have been reported in recent years. Furthermore, protein-protein interactions and multi-omics integrated analysis were carried out to explore the important metabolites and proteins that involved in significant pathways in the progression of COPD for explanation the pathogenesis of COPD. Finally, the prospective and challenges in the study of COPD were proposed. It is expected that this review will provide some references for the development of diagnostic methods and elucidation of the pathogenesis of COPD.

Metabolomic profiling of anaerobic and aerobic energy metabolic pathways in chronic obstructive pulmonary disease

While there is no cure for chronic obstructive pulmonary disease (COPD), its progressive nature and the formidable challenge to manage its symptoms warrant a more extensive study of the pathogenesis and related mechanisms. A new emphasis on COPD study is the change of energy metabolism. For the first time, this study investigated the anaerobic and aerobic energy metabolic pathways in COPD using the metabolomic approach. Metabolomic analysis was used to investigate energy metabolites in 140 COPD patients. The significance of energy metabolism in COPD was comprehensively explored by the Global Initiative for Chronic Obstructive Lung Disease-GOLD grading, acute exacerbation vs. stable phase (either clinical stability or four-week stable phase), age group, smoking index, lung function, and COPD Assessment Test (CAT) score. Through comprehensive evaluation, we found that COPD patients have a significant imbalance in the aerobic and anaerobic energy metabolisms in resting state, and a high tendency of anaerobic energy supply mechanism that correlates positively with disease progression. This study highlighted the significance of anaerobic and low-efficiency energy supply pathways in lung injury and linked it to the energy-inflammation-lung ventilatory function and the motion limitation mechanism in COPD patients, which implies a novel therapeutic direction for this devastating disease.

The Role of Human Leukocyte Antigen-DR in Regulatory T Cells in Patients with Virus-Induced Acute Exacerbation of Chronic Obstructive Pulmonary Disease

Background

This study assessed the role of different immune phenotypes of T cells in virus-induced acute exacerbation of chronic obstructive pulmonary disease (AECOPD).

Material/Methods

The study involved 103 participants, including individuals with virus-induced AECOPD (n=32), non-virus-induced AECOPD (n=31), and stable COPD (n=20) and individuals who were healthy smokers (n=20). The immune phenotypes of T cells in peripheral blood were evaluated via flow cytometry analysis, and the differences were analyzed.

Results

Patients with virus-induced AECOPD (virus group) had a higher COPD assessment test score on admission than those in the group with non-virus-induced AECOPD (nonvirus group; 25.6±3.8 vs 21.9±4.8, P=0.045). A lower CD4⁺ human leukocyte antigen-DR (HLA-DR)⁺ frequency was found in the peripheral blood of the virus group compared with the nonvirus group (2.2 vs 4.2, P=0.015), and the frequency of CD4⁺ CD25^high CD127^low HLA-DR⁺ in CD4⁺ in the virus group was lower than in the nonvirus group (1.1 vs 3.6, P=0.011). The CD3⁺, CD4⁺, CD8⁺, CD4⁺ central memory T cell, CD4⁺ effector memory T cell (Tem), CD4⁺ end-stage T cell, and CD8⁺ Tem levels in lymphocytes of peripheral blood were lower in exacerbation groups relative to those in the stable COPD and healthy smoking groups, but similar between exacerbation groups. Similar frequencies and levels of T cells between different stagings of COPD were also identified.

Conclusions

The expression of HLA-DR on the cell surface of CD4⁺ regulatory T cells (Tregs) was lower in the peripheral blood of patients with virus-induced AECOPD. The expression of HLA-DR in CD4⁺ Tregs suggested the effect of respiratory viruses on adaptive immunity of patients with AECOPD to some extent.

Bronchial Variation: Anatomical Abnormality May Predispose Chronic Obstructive Pulmonary Disease

Noxious particulate matter in the air is a primary cause of chronic obstructive pulmonary disease (COPD). The bronchial tree acts to filter these materials in the air and preserve the integrity of the bronchi. Accumulating evidence has demonstrated that smoking and air pollutants are the most prominent risk factors of COPD. Bifurcations in the airway may act as deposition sites for the retention of inhaled particles, however, little is known concerning the impacts of abnormalities of the bronchial anatomy in the pathogenesis of COPD. Studies have reported significant associations between bronchial variations and the symptoms in COPD. In particular, it has been shown that bronchial variations in the central airway tree may contribute to the development of COPD. In this review, we identified three common types of bronchial variation that were used to formulate a unifying hypothesis to explain how bronchial variations contribute to the development of COPD. We also investigated the current evidence for the involvement of specific genes including fibroblast growth factor 10 (Fgf10) and bone morphogenetic protein 4 (Bmp4) in the formation of bronchial variation. Finally, we highlight novel assessment strategies and opportunities for future research of bronchial variations and genetic susceptibility in COPD and comorbidities. Our data strongly highlight the role of bronchial variations in the development, complications, and acute exacerbation of COPD.

Transcriptomics analysis for the identification of potential age-related genes and cells associated with three major urogenital cancers

Age is one of the most important risk factors of the occurrence for tumor patients. The majority of patients with urogenital cancers are the elderly, whose clinical characteristics are greatly affected by age and ageing. Our study aimed to explore age-related genes, cells, and biological changes in three common urogenital cancers via integrative bioinformatics analysis. First, mRNA (count format) and clinical data for bladder cancer, prostate cancer and renal cell carcinoma were downloaded from the Cancer Genome Atlas (TCGA). Through the comparison of clinicopathological characteristics, genes expression and cells infiltration between the old group and the young group, it was found that the clinical characteristics, genes and cells in the tumor microenvironment of different ages were quite different. And 4 key cells, 14 hub genes and some potential pathways were identified and considered as important factors. More importantly, we analyzed the differential landscape of the genes and cells from different perspectives, and confirmed its importance. In conclusion, we identified genes and cell types associated with age-related changes in the tumour microenvironment in urogenital cancer patients. These genes and cell types may play a critical role in the age-associated differences in clinicopathological characteristics among urogenital cancers, thus providing a link between ageing and cancer occurrence. The findings of this study may pave the way for the development of age-tailored approaches to treat cancer and other age-related diseases.

Mechanisms of interactions between lung-origin telocytes and mesenchymal stem cells to treat experimental acute lung injury

Acute lung injury is a serious form and major cause of patient death and still needs efficient therapies. The present study evidenced that co-transplantation of mesenchymal stem cells (MSCs) and telocytes (TCs) improved the severity of experimental lung tissue inflammation, edema, and injury, where TCs increased MSCs migration into the lung and the capacity of MSCs proliferation and movement. Of molecular mechanisms, Osteopontin-dominant networks were active in MSCs and TCs, and might play supportive and nutrimental roles in the interaction between MSCs and TCs, especially activated TCs by lipopolysaccharide. The interaction between epidermal growth factor and its receptor from MSCs and TCs could play critical roles in communications between MSCs and TCs, responsible for MSCs proliferation and movement, especially after inflammatory activation. Our studies provide the evidence that TCs possess nutrimental and supportive roles in implanted MSCs, and co-transplantation of MSCs and TCs can be a new alternative in the therapy of acute lung injury.

Immunological and clinicopathological characteristics of C1RL in 2120 glioma patients

BACKGROUND

Glioma is a deadly and immunosuppressive brain tumour. Complement C1r subcomponent like (C1RL), a prognostic biomarker in several kinds of tumours, has attracted increasing attention from oncologists. However, the role of C1RL in glioma remains unclear.

METHODS

Through analysis of 2120 glioma patients from 5 public datasets, the relationships between C1RL expression and clinicopathological characteristics were evaluated. Furthermore, the C1RL-associated genes were screened, and Gene Ontology (GO) analysis was conducted to investigate biological process enrichment. In addition, tumour purity, leukocyte infiltration and overall survival were evaluated based on C1RL expression.

RESULTS

We found that C1RL expression was upregulated in glioblastoma (GBM), especially mesenchymal GBM and primary GBM. Increased C1RL expression accompanied the IDH1-wt phenotype in both lower grade glioma (LGG) and GBM. C1RL- associated genes were mainly enriched in biological processes related to the immune response. C1RL expression was also correlated with reduced tumour purity and increased M2 macrophage infiltration. Higher C1RL expression predicted unfavourable survival in patients with glioma and therapeutic resistance in GBM.

CONCLUSIONS

Our results imply that C1RL is involved in immunological activities and is an independent unfavourable prognostic biomarker in patients with glioma. C1RL is a potential clinical immunotherapeutic target for glioma treatment in the future.

Research Advances on DNA Methylation in Idiopathic Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is a chronic complex lung disease with no specific treatment and poor prognosis, characterized by the pulmonary progressive fibrosis and dysfunctions that lead to respiratory failure. Several factors may impact the progress of IPF, including age, cigarette smoking, and dusts, of which genetic and epigenetic factors mainly contribute to lung tissue fibrosis. DNA methylation is one of epigenetic processes that occur in many diseases and regulate chromosomal and extrachromosomal DNA functions in response to environmental exposures. The methylation plays pivotal roles in regulation of gene expression to facilitate the formation of fibroblastic foci and lung fibrosis. This chapter will describe alterations and effects of the DNA methylation on gene expression, the potential application of DNA methylation as a biomarker, and significance as therapeutic targets. Those understanding will provide us new insight into the treatment and prognosis of IPF.

Trans-omic profiling between clinical phenoms and lipidomes among patients with different subtypes of lung cancer

Lung cancer has high mortality, often accompanied with systemic metabolic disorders. The present study aimed at defining values of trans-nodules cross-clinical phenomic and lipidomic network layers in patients with adenocarcinoma (ADC), squamous cell carcinomas, or small cell lung cancer (SCLC). We measured plasma lipidomic profiles of lung cancer patients and found that altered lipid panels and concentrations varied among lung cancer subtypes, genders, ages, stages, metastatic status, nutritional status, and clinical phenome severity. It was shown that phosphatidylethanolamine elements (36:2, 18:0/18:2, and 18:1/18:1) were SCLC specific, whereas lysophosphatidylcholine (20:1 and 22:0 sn-position-1) and phosphatidylcholine (19:0/19:0 and 19:0/21:2) were ADC specific. There were statistically more lipids declined in male, <60 ages, late stage, metastasis, or body mass index < 22 . Clinical trans-omics analyses demonstrated that one phenome in lung cancer subtypes might be generated from multiple metabolic pathways and metabolites, whereas a metabolic pathway and metabolite could contribute to different phenomes among subtypes, although those needed to be furthermore confirmed by bigger studies including larger population of patients in multicenters. Thus, our data suggested that trans-omic profiles between clinical phenomes and lipidomes might have the value to uncover the heterogeneity of lipid metabolism among lung cancer subtypes and to screen out phenome-based lipid panels as subtype-specific biomarkers.

Xiaoqinglong Decoction Protects the Lungs of AECOPD Mice through the AMPK/mTOR Signaling Pathway

Method

Male C57BL/6J mice were used to establish AECOPD model by cigarette smoke and bacterial exposure. Mice were randomly divided into normal control (NC), AECOPD, XQLD, Compound C (Com C), Com C + XQLD, and Clarithromycin (CLA) groups. After treatment, the pulmonary function was evaluated by whole-body plethysmograph. The lung histopathology was observed by HE staining. The serum levels of IL-6, TNF-α, and COX-2 were detected by ELISA assay. The apoptotic index was measured by TUNEL assay, and the protein expressions of Bax, Bcl-2, Caspase-3, GRP78, and CHOP in the lung tissues were measured by western blot assay.

Results

XQLD treatment can improve pulmonary function (PF), ameliorate lung injury, and suppress inflammation and apoptosis of lung tissues. In addition, XQLD also markedly attenuated endoplasmic reticulum stress (ERS) and activated AMPK/mTOR pathway in the lung tissues of mice with AECOPD. However, the AMPK inhibitor Compound C decreased the protective effect of XQLD in AECOPD mice.

Conclusion

These findings suggested that XQLD has protective effect against inflammation and apoptosis in AECOPD mice by attenuating ER stress via AMPK/mTOR pathway.

Association of mutation and low expression of the CTCF gene with breast cancer progression

Background

CTCF encodes 11-zinc finger protein which is implicated in multiple tumors including the carcinoma of the breast. The Present study investigates the association of CTCF mutations and their expression in breast cancer cases.

Methods

A total of 155 breast cancer and an equal number of adjacent normal tissue samples from 155 breast cancer patients were examined for CTCF mutation(s) by PCR-SSCP and automated DNA sequencing. Immunohistochemistry (IHC) method was used to analyze CTCF expression. Molecular findings were statistically analyzed with various clinicopathological features to identify associations of clinical relevance.

Results

Of the total, 16.1% (25/155) cases exhibited mutation in the CTCF gene. Missense mutations Gln > His (G > T) in exon 1 and silent mutations Ser > Ser (C > T) in exon 4 of CTCF gene were analyzed. A significant association was observed between CTCF mutations and some clinicopathological parameters namely menopausal status (p = 0.02) tumor stage (p = 0.03) nodal status (p = 0.03) and ER expression (p = 0.04). Protein expression analysis showed 42.58% samples having low or no expression (+), 38.0% with moderate (++) expression and 19.35% having high (+++) expression for CTCF. A significant association was found between CTCF protein expression and clinicopathological parameters include histological grade (p = 0.04), tumor stage (p = 0.04), nodal status (p = 0.03) and ER status (p = 0.04).

Conclusions

The data suggest that CTCF mutations leading to its inactivation significantly contribute to the progression of breast cancer.

Protein Network Analysis Identifies Changes in the Level of Proteins Involved in Platelet Degranulation, Proteolysis and Cholesterol Metabolism Pathways in AECOPD Patients

Chronic obstructive pulmonary disease (COPD) is characterised by a progressive pulmonary and systemic inflammation. Acute exacerbations of COPD (AECOPD) are associated with acute inflammation and infection, increase in the rates of morbidity and mortality. Previous proteomic studies have focussed on identifying proteins involved in COPD pathogenesis in samples collected from the lung (e.g. lung tissue biopsies, bronchoalveolar lavage and sputum) but not from blood of patients who experienced AECOPD. In this study, plasma was analysed by two independent quantitative proteomics techniques; isobaric tag for relative and absolute quantitation (iTRAQ) and multiple reaction monitoring (MRM) to identify differential expression of circulating proteins in patients with stable COPD (sCOPD) and AECOPD. Firstly, iTRAQ performed on pooled plasma samples from AECOPD, sCOPD, and healthy non-smoking controls (HC) revealed 15 differentially expressed proteins between the 3 groups. MRM subsequently performed on a separate cohort of AECOPD, sCOPD, and HC patients confirmed 9 proteins to be differentially expressed by AECOPD compared to HC (Afamin, alpha-1-antichymotrypsin, Apolipoprotein E, Beta-2-glycoprotein 1, Complement component C9, Fibronectin, Immunoglobulin lambda like polypeptide 5, Inter-alpha-trypsin inhibitor heavy chain H3, Leucine rich alpha-2-glycoprotein 1). Network analysis demonstrates that most of these proteins are involved in proteolysis regulation, platelet degranulation and cholesterol metabolism. In conclusion, several potential plasma biomarkers for AECOPD were identified in this study. Further validation studies of these proteins may elucidate their roles in the development of AECOPD.

Molecular regulation and clinical significance of caveolin-1 methylation in chronic lung diseases

Chronic lung diseases represent a largely global burden whose pathogenesis remains largely unknown. Research increasingly suggests that epigenetic modifications, especially DNA methylation, play a mechanistic role in chronic lung diseases. DNA methylation can affect gene expression and induce various diseases. Of the caveolae in plasma membrane of cell, caveolin-1 (Cav-1) is a crucial structural constituent involved in many important life activities. With the increasingly advanced progress of genome-wide methylation sequencing technologies, the important impact of Cav-1 DNA methylation has been discovered. The present review overviews the biological characters, functions, and structure of Cav-1; epigenetic modifications of Cav-1 in health and disease; expression and regulation of Cav-1 DNA methylation in the respiratory system and its significance; as well as clinical potential as disease-specific biomarker and targets for early diagnosis and therapy.

Clinical lipidomics in understanding of lung cancer: Opportunity and challenge

Disordered lipid metabolisms have been evidenced in lung cancer as well as its subtypes. Lipidomics with in-depth mining is considered as a critical member of the multiple omics family and a lipid-specific tool to understand disease-associated lipid metabolism and disease-specific dysfunctions of lipid species, discover biomarkers and targets for monitoring therapeutic strategies, and provide insights into lipid profiling and pathophysiological mechanisms in lung cancer. The present review describes the characters and patterns of lipidomic profiles in patients with different lung cancer subtypes, important values of comprehensive lipidomic profiles in understanding of lung cancer heterogeneity, urgent needs of standardized methodologies, potential mechanisms by lipid-associated enzymes and proteins, and the importance of integration between clinical phenomes and lipidomic profiles. The characteristics of lipidomic profiles in different lung cancer subtypes are extremely varied among study designs, objects, methods, and analyses. Preliminary data from recent studies demonstrate the specificity of lipidomic profiles specific for lung cancer stage, severity, subtype, and response to drugs. The heterogeneity of lipidomic profiles and lipid metabolism may be part of systems heterogeneity in lung cancer and be responsible for the development of drug resistance, although there are needs for direct evidence to show the existence of intra- or inter-lung cancer heterogeneity of lipidomic profiles. With an increasing understanding of expression profiles of genes and proteins, lipidomic profiles should be associated with activities of enzymes and proteins involved in the processes of lipid metabolism, which can be profiled with genomics and proteomics, and to provide the opportunity for the integration of lipidomic profiles with gene and protein expression profiles. The concept of clinical trans-omics should be emphasized to integrate data of lipidomics with clinical phenomics to identify disease-specific and phenome-specific biomarkers and targets, although there are still a large number of challenges to be overcome in the integration between clinical phenomes and lipidomic profiles.

Identification of differentially expressed genes and signaling pathways in chronic obstructive pulmonary disease via bioinformatic analysis

Chronic obstructive pulmonary disease (COPD) is a multifactorial and heterogeneous disease that creates public health challenges worldwide. The underlying molecular mechanisms of COPD are not entirely clear. In this study, we aimed to identify the critical genes and potential molecular mechanisms of COPD by bioinformatic analysis. The gene expression profiles of lung tissues of COPD cases and healthy control subjects were obtained from the Gene Expression Omnibus. Differentially expressed genes were analyzed by integration with annotations from Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, followed by construction of a protein‐protein interaction network and weighted gene coexpression analysis. We identified 139 differentially expressed genes associated with the progression of COPD, among which 14 Hub genes were identified and found to be enriched in certain categories, including immune and inflammatory response, response to lipopolysaccharide and receptor for advanced glycation end products binding; in addition, these Hub genes are involved in multiple signaling pathways, particularly hematopoietic cell lineage and cytokine‐cytokine receptor interaction. The 14 Hub genes were positively or negatively associated with COPD by wgcna analysis. The genes CX3CR1,PTGS2,FPR1,FPR2, S100A12,EGR1,CD163, S100A8 and S100A9 were identified to mediate inflammation and injury of the lung, and play critical roles in the pathogenesis of COPD. These findings improve our understanding of the underlying molecular mechanisms of COPD.

Roles of cohesin in chromosome architecture and gene expression

Cohesin-mediated chromatin organization plays an important role in formation and stabilization of chromosome architecture and gene regulation. Mechanisms by which cohesin shapes chromosome and regulates gene expression remain unclear. The present article overviews biological characters and functions of cohesin and core subunits and explores roles of regulatory factors (e.g. Pds5, Wapl, and Eco1) in dynamic behaviors of cohesin. Cohesin interacts with CCCTC binding factor (CTCF) and other factors to maintain and stabilize multi-dimensional organizations of topological loops and distances between sites during cell segmentation. We also describe functional roles of cohesin in cell cycle by entrapping sister chromatids to form embrace and handcuff models, loading onto chromatin, establishing cohesion function, and regulating removal of cohesin and associated factors from the chromosome arm through prophase pathway or at onset of anaphase. It is questioned whether those factors associated with cohesin-regulated processes can be identified as biology- or disease-specific biomarkers and druggable targets to dynamically monitor changes during phasing, staging, progressing, and responding of diseases. It is also expected to explore heterogenetic roles of cohesin between single cells and regulatory roles of cohesin in trans-omic profiles and functions. Further understanding of cohesin functions will be beneficial to improve diagnosis and treatment of cohesinopathies.

A tour of 3D genome with a focus on CTCF

The complex three-dimensional (3D) structure of the genome plays critical roles in the maintenance of genome stability, organization, and dynamics and in regulation of gene expression for understanding molecular mechanisms and diseases. Chromatin maintains biological functions and transcriptional activities through long distance interaction and interactions between loops and enhancers-promoters. We firstly overview the architecture and biology of chromatin and loops, topologically associated domains (TADs) and interactions, and compartments and functions. We specifically focus on CCCTC-binding factor (CTCF) in 3D genome organization and function to furthermore understand the significance of CTCF biology, transcriptional regulations, interactions with cohesin, roles in DNA binding, influences of CTCF degradation, and communication with wings-apart like (Wapl) protein. We also summarize the advanced single cell approaches to further monitor dynamics of CTCF functions and structures in the maintenance of 3D genome organization and function at single cell level.

Values of integration between lipidomics and clinical phenomes in patients with acute lung infection, pulmonary embolism, or acute exacerbation of chronic pulmonary diseases: a preliminary study

Background

The morbidity and mortality of patients with critical illnesses remain high in pulmonary critical care units and a poorly understood correlation between alterations of lipid elements and clinical phenomes remain unelucidated.

Methods

In the present study, we investigated plasma lipidomic profiles of 30 patients with severe acute pneumonia (SAP), acute pulmonary embolism (APE), and acute exacerbation of chronic pulmonary diseases (AECOPD) or 15 healthy with the aim to compare disease specificity of lipidomic patterns. We defined the specificity of lipidomic profiles in SAP by comparing it to both APE and AECOPD. Analysis of the correlation between altered lipid elements and clinical phenotypes using the lipid-QTL model was then carried out.

Results

We integrated lipidomic profiles with clinical phenomes measured by score values from the digital evaluation score system and found phenome-associated lipid elements to identify disease-specific lipidomic profiling. The present study demonstrates that lipidomic profiles of patients with acute lung diseases are different from healthy lungs, and there are also disease-specific portions of lipidomics among SAP, APE, or AECOPD. The comprehensive profiles of clinical phenomes or lipidomics are valuable in describing the disease specificity of patient phenomes and lipid elements. The combination of clinical phenomes with lipidomic profiles provides more detailed disease-specific information on panels of lipid elements When compared to the use of each separately.

Conclusions

Integrating biological functions with disease specificity, we believe that clinical lipidomics may create a new alternative way to understand lipid-associated mechanisms of critical illnesses and develop a new category of disease-specific biomarkers and therapeutic targets.

Electronic supplementary material

The online version of this article (10.1186/s12967-019-1898-z) contains supplementary material, which is available to authorized users.

Interferon gamma induces inflammatory responses through the interaction of CEACAM1 and PI3K in airway epithelial cells

BACKGROUND

Interferon gamma (IFNγ) plays an important role in the development of chronic lung diseases via the production of inflammatory mediators, although the exact mechanism remains unclear. The present study aimed at investigating the potential mechanisms by which IFNγ induced over-production of interleukins through the interaction between carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) and phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) pathway.

METHODS

IFN-γ induced over-production of interleukin (IL) 6 and IL8, and RNA expression of CEACAM1 and its subtypes or PI3K and its subtypes in human bronchial epithelial cells (HBE). The production of IL6 and IL8 or cell proliferation and movement were also evaluated in cell^CEACAM1- or cell^CEACAM1+ after the induction of IFN-γ. Roles of PI3K subtype proteins, e.g. PI3Kp110α/δ, Akt, p110α/γ/δ/β/mTOR, PI3Kp110α/δ/β, PI3Kp110δ, or pan-PI3K in IFN-γ-induced CEACAM1 subtype alterations were furthermore validated using those proteins of PI3K subtypes.

RESULTS

CEACAM1, especially CEACAM1-S isoforms, was significantly up-regulated in HBE cells after treatment with IFN-γ. CEACAM1 played roles in expression of IL-6 and IL-8, and facilitated cellular proliferation and migration. IFN-γ up-regulated the expression of CEACAM1 in airway epithelial cells, especially CEACAM1-S isoforms, promoting cellular proliferation, migration, and the production of inflammatory factors. PI3K (p110δ)/Akt/mTOR pathway was involved in the process of IFN-γ-upregulated CEACAM1, especially CEACAM1-S. On the other hand, CEACAM1 could promote the activation of PI3K/Akt/mTOR pathway.

CONCLUSION

IFN-γ could induce inflammatory responses, cellular growth and proliferation through the interaction of CEACAM1 (especially CEACAM1-S isoforms) and PI3K(p110δ)/Akt/mTOR in airway epithelial cells, which might be new alternative of future therapies against epithelial transition from inflammation to cancer.

Efficacy and safety of Xuebijing injection and its influence on immunomodulation in acute exacerbations of chronic obstructive pulmonary disease: study protocol for a randomized controlled trial

Background

Acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is the leading cause of mortality in chronic obstructive pulmonary disease (COPD). Traditional Chinese medicine (TCM) has been widely used in Asia as an adjunct treatment for AECOPD to improve the patients’ symptoms. Xuebijing (XBJ) injection is one of the major herbal medicines used in TCM. Previous small-sample clinical trials have proven its efficacy and safety in the treatment of AECOPD; however, the current data on XBJ as an adjunct therapy are insufficient. The present study will be a multi-center randomized clinical trial (RCT) to evaluate the efficacy and safety of XBJ injection in AECOPD and explore its influence on the immune function based on the altered levels of T cells.

Methods

This study will be a prospective, randomized, placebo-controlled, blinded, multi-center trial. A total of 300 eligible patients will be randomly assigned to the treatment or placebo control group in a 1:1 ratio using a central randomization system. The treatment group will receive routine medication plus XBJ injection, and the control group will receive routine medication plus 0.9% NaCl injection. The patients will receive the corresponding treatment for 5 days starting within 24 h of enrollment. The primary outcome, the of rate endotracheal intubation, will be evaluated on day 28 after treatment. The secondary outcomes will include changes in immune and inflammatory indicators, respiratory support, mortality rate after 28 days, blood gas analysis, improvement in Acute physiology and chronic health evaluation (APACHE) II scores and clinical symptoms, and the length and cost of intensive care unit stay and hospitalization. The safety of the interventions will be assessed throughout the trial.

Discussion

This is the first and largest randomized, controlled, blinded trial that evaluates the efficacy of XBJ injection as adjuvant therapy for AECOPD. The results of this trial will provide valuable clinical evidence for recommendations on the management of the disease and identify the underlying mechanisms.

Trial registration

ClinicalTrials.gov, NCT02937974. Registered on 13 October 2016. Chinese clinical trial registry, ChiCTR-IPR-17011667. Registered on 15 June 2017.

Electronic supplementary material

The online version of this article (10.1186/s13063-019-3204-z) contains supplementary material, which is available to authorized users.

Single Cell Proteomics for Molecular Targets in Lung Cancer: High-Dimensional Data Acquisition and Analysis

In the proteomic and genomic era, lung cancer researchers are increasingly under challenge with traditional protein analyzing tools. High output, multiplexed analytical procedures are in demand for disclosing the post-translational modification, molecular interactions and signaling pathways of proteins precisely, specifically, dynamically and systematically, as well as for identifying novel proteins and their functions. This could be better realized by single-cell proteomic methods than conventional proteomic methods. Using single-cell proteomic tools including flow cytometry, mass cytometry, microfluidics and chip technologies, chemical cytometry, single-cell western blotting, the quantity and functions of proteins are analyzed simultaneously. Aside from deciphering disease mechanisms, single-cell proteomic techniques facilitate the identification and screening of biomarkers, molecular targets and promising compounds as well. This review summarized single-cell proteomic tools and their use in lung cancer.

Emergence of Bias During the Synthesis and Amplification of cDNA for scRNA-seq

The advent of single-cell omics technology has promoted our understanding of the genomic, epigenomic, and transcriptomic heterogeneity in individual cells. Compared to traditional sequencing studies using bulk cells, single-cell transcriptome technology is naturally more dynamic for in depth analysis of genomic variation resulting from cell division and is useful in unraveling the regulatory mechanisms of gene networks in many diseases. However, there are still some limitations of current single-cell RNA sequencing (scRNA-seq) protocols. Biases that arise during the RNA reverse transcription and cDNA pre-amplification steps are the most common problems and play pivotal roles in limiting the quantitative accuracy of scRNA-seq. In this review, we will describe how these biases emerge and impact scRNA-seq protocols. Moreover, we will introduce several current and convenient modified scRNA-seq methods that allow for bias to be decreased and estimated.

Detection and Application of RNA Editing in Cancer

RNA editing is the process which happened in the post-transcriptional stage that the genetic information contained in an RNA molecule will be changed. RNA editing has been found to be related with many cancers, so through identifying RNA editing sites, we can find useful information on the process of carcinogenesis. In this review, we will discuss the main types of RNA editing and their role in cancers, as well as the current detection methods of RNA editing and the challenges we should overcome.

Heterogeneity of lipidomic profiles among lung cancer subtypes of patients

Lung cancer is a leading cause of cancer-related deaths with an increasing incidence and poor prognoses. To further understand the regulatory mechanisms of lipidomic profiles in lung cancer subtypes, we measure the profiles of plasma lipidome between health and patients with lung cancer or among patients with squamous cell carcinomas, adenocarcinoma or small cell lung cancer and to correct lipidomic and genomic profiles of lipid-associated enzymes and proteins by integrating the data of large-scale genome screening. Our studies demonstrated that circulating levels of PS and lysoPS significantly increased, while lysoPE and PE decreased in patients with lung cancer. Our data indicate that lung cancer-specific and subtype-specific lipidomics in the circulation are important to understand mechanisms of systemic metabolisms and identify diagnostic biomarkers and therapeutic targets. The carbon atoms, dual bonds or isomerism in the lipid molecule may play important roles in lung cancer cell differentiations and development. This is the first try to integrate lipidomic data with lipid protein-associated genomic expression among lung cancer subtypes as the part of clinical trans-omics. We found that a large number of lipid protein-associated genes significantly change among cancer subtypes, with correlations with altered species and spatial structures of lipid metabolites.

Searching for biomarkers of chronic obstructive pulmonary disease using proteomics: The current state

Detection of proteins which may be potential biomarkers of disorders represents a big step forward in understanding the molecular mechanisms that underlie pathological processes. In this context proteomics plays the important role of opening a path for the identification of molecular signatures that can potentially assist in early diagnosis of several clinical disturbances. Aim of this report is to provide an overview of the wide variety of proteomic strategies that have been applied to the investigation of chronic obstructive pulmonary disease (COPD), a severe disorder that causes an irreversible damage to the lungs and for which there is no cure yet. The results in this area published over the past decade show that proteomics indeed has the ability of monitoring alterations in expression profiles of proteins from fluids/tissues of patients affected by COPD and healthy controls. However, these data also suggest that proteomics, while being an attractive tool for the identification of novel pathological mediators of COPD, remains a technique mainly generated and developed in research laboratories. Great efforts dedicated to the validation of these biological signatures will result in the proof of their clinical utility.

The advances in CRISPR technology and 3D genome

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system is a prokaryotic immune system that used to resist foreign genetic factors. It rapidly becomes the hot technology in life sciences and is applies for genome editing to solve the problem of genome-derived diseases. Using CRISPR/Cas technique, the biological DNA sequence can be repaired, cut, replaced, or added. It can effectively change the human stem cells and is expected to achieve results in the treatment. Compared with ZFN and TALEN genome editing techniques, CRISPR is more effective, accurate, and convenient. The application of CRISPR technique in three dimensional (3D) genome structure makes us understand the relationship between linear DNA sequence and 3D chromatin structure. Utilizing CRISPR/Cas9 genome editing to reverse or delete CTCF binding sites, to recognize changes of topological isomerism of the genome and interactions between chromatin loops. The purpose of this review is to introduce the characteristics and classification of the current CRISPR/Cas system, multiple functions, and potential therapeutic uses, as well as to outline the effect of the technique on chromatin loops by changing CTCF sites in 3D genomes. We will also briefly describe the importance of ethical dilemmas to be faced in CRISPR applications and provide a perspective for potential CRISPR considerations.

Roles of NIPBL in maintenance of genome stability

A cohesin-loading factor (NIPBL) is one of important regulatory factors in the maintenance of 3D genome organization and function, by interacting with a large number of factors, e.g. cohesion, CCCTC-binding factor (CTCF) or cohesin complex component. The present article overviews the critical and regulatory roles of NIBPL in cohesion loading on chromotin and in gene expression and transcriptional signaling. We explore molecular mechanisms by which NIPBL recruits endogenous histone deacetylase (HDAC) to induce histone deacetylation and influence multi-dimensions of genome, through which NIPBL "hop" movement in chromatin regulates gene expression and alters genome folding. NIPBL regulates the process of CTCF and cohesion into chromatin loops and topologically associated domains, binding of cohesion and H3K4mes3 through interaction among promoters and enhancers. HP1 recruits NIPBL to DNA damage site through RNF8/RNF168 ubiquitylation pathway. NIPBL contributes to regulation of genome-controlled gene expression through the influence of cohesin in chromosome structure. NIPBL interacts with cohesin and then increases transcriptional activities of REC8 promoter, leading to up-regulation of gene expression. NIPBL movement among chromosomal loops regulates gene expression through dynamic alterations of genome organization. Thus, we expect a new and deep insight to understand dynamics of chromosome and explore potential strategies of therapiesc on basis of NIPBL.

The role of nuclear matrix protein HNRNPU in maintaining the architecture of 3D genome

The complexity of higher eukaryote genomes is far from being explained by linear information. There is a need to understand roles of genome regulation at the organism level through defining a comprehensive profile of chromosomal organization. Chromosome conformation capture (3C)-based studies reveal that higher-order of chromatin include not only long-range chromatin loops, but also compartments and topologically associating domains as the basis of genome structure and functions. However, the molecular machinery how the genome is spatially organized is still inadequate. Exciting progress has been made with the development of today's technology, we find that heterogeneous nuclear ribonucleoprotein U, initially identified as a structural nuclear protein, plays important role in three-dimensional (3D) genome organization by high-throughput assays. The disruption of this protein not only results in compartment switching on of the genome, it also reduces of TAD boundary strengths at borders between two types of compartments, and regulates chromatin loop by decrease its intensities. In addition, HNRNPU mainly binds to active chromatin. Most of HNRNPU peaks is consistent with CTCF or RAD21.It also plays an irreplaceable role in the processes of mitosis. This review aims to discuss the role of HNRNPU in maintaining the 3D chromatin architecture, as well as the recent development and human diseases involved in this nuclear matrix (NM)-associated protein.

3D genomic regulation of lncRNA and Xist in X chromosome

Long noncoding RNAs (lncRNAs) act as important regulators in cardiovascular diseases, neural degenerative disease, or cancers, by localizing and spreading across chromatins. lncRNA can regulate the 3D architecture of the enhancer cluster at the target gene locus, relevant to analogous lncRNA-protein coding gene pairs. X inactive specific transcript (Xist) plays a critical role in the process and biological function of lncRNAs. The lncRNA Jpx, Xist activator, is a nonprotein-coding RNA transcribed from a gene within the X-inactivation center and acts as a numerator element to control X-chromosome number and activate Xist transcription by interacting with CCCTC-binding factor. Up-regulated lncRNA Xist initiates X chromosome inactivation process and attracts specific chromatin modifiers. A number of chromatin-modified factors interact with lncRNAs modify 3D genome architecture and mediate Xist function in embryo development. Thus, the regulation of lncRNAs in 3D genome progresses is the key mechanism of Xist, as a therapeutic potential for Xist associated diseases.

The Significance of Single-Cell Biomedicine in Stem Cells

Clinical application of stem cells (SCs) progresses significantly in the treatment of a large number of diseases, e.g. leukemia, respiratory diseases, kidney disease, cerebral palsy, autism, or autoimmune diseases. Of those, the population, biological phenotypes, and functions of individual SCs are mainly concerned, due to the lack of cell separation and purification processes. The single-cell technology, including microfluidic technology and single-cell genome amplification technology, is widely used to study SCs and gains some recognitions. The present review will address the importance of single-cell technologies in the recognition and heterogeneity of SCs and highlight the significance of current single-cell approaches in the understanding of SC phenotypes. We also discuss the values of single-cell studies to overcome the bottleneck in explore of biological mechanisms and reveal the therapeutic potentials of SCs in diseases, especially tumor-related diseases, as new diagnostic and therapeutic strategies.

Significance of Mitochondria DNA Mutations in Diseases

Mitochondria are essential double-membraned cytoplasmic organelles to support aerobic respiration and produce cellular energy by oxidative phosphorylation (OXPHOS). Mitochondrial functions are controlled by mitochondrial (mtDNA) and nuclear genomes (nDNA). Mutations of mtDNA result in mitochondrial dysfunction and multisystem diseases through compromising OXPHOS function directly by a point mutation or a large-scale mtDNA rearrangement. One or more of OXPHOS complexes are impaired and dysfunctional to affect tissues with high energy demands. mtDNA is more susceptible to oxidative damage and has more mutations than nDNA. Unlike diploid nDNA, mtDNA is a multi-copy genome transmitted and maternally inherited through oocyte. The multi-copy nature of mtDNA easily causes the heteroplasmy as a unique aspect of mtDNA, making mitochondrial diseases more complex and heterogeneous. mtDNA-associated mitochondrial dysfunction plays the important role in the development of multisystemic primary mitochondrial disease, neurodegeneration, and cancer. The present article overviews the occurrence of mtDNA mutation, interactions with other factors, and molecular mechanisms of mtDNA-associated diseases.