Significance of bioinformatics in research of chronic obstructive pulmonary disease

Integration of multi-omics datasets enables molecular classification of COPD

Chronic obstructive pulmonary disease (COPD) is an umbrella diagnosis caused by a multitude of underlying mechanisms, and molecular sub-phenotyping is needed to develop molecular diagnostic/prognostic tools and efficacious treatments.The objective of these studies was to investigate whether multi-omics integration improves the accuracy of molecular classification of COPD in small cohorts.Nine omics data blocks (comprising mRNA, micro RNA, proteomes and metabolomes) collected from several anatomical locations from 52 female subjects were integrated by similarity network fusion (SNF). Multi-omics integration significantly improved the accuracy of group classification of COPD patients from healthy never-smokers and from smokers with normal spirometry, reducing required group sizes from n=30 to n=6 at 95% power. Seven different combinations of four to seven omics platforms achieved >95% accuracy.For the first time, a quantitative relationship between multi-omics data integration and accuracy of data-driven classification power has been demonstrated across nine omics data blocks. Integrating five to seven omics data blocks enabled 100% correct classification of COPD diagnosis with groups as small as n=6 individuals, despite strong confounding effects of current smoking. These results can serve as guidelines for the design of future systems-based multi-omics investigations, with indications that integrating five to six data blocks from several molecular levels and anatomical locations suffices to facilitate unsupervised molecular classification in small cohorts.

Application of clinical bioinformatics in lung cancer-specific biomarkers

The fact that lung cancer is a heterogeneous disease suggests that there is a high likelihood that effective lung cancer biomarkers will need to address patient-specific molecular defects, clinical characters, and aspects of the tumor microenvironment. In this transition, clinical bioinformatics tools and resources are the most appropriate means to improve the analysis, as major biological databases are now containing clinical data alongside genomics, proteomics, and other biological data. Clinical bioinformatics comprises a series of concepts and approaches that have been used successfully both to delineate novel biological mechanisms and to drive translational advances in individualized healthcare. In this article, we outline several of emerging clinical bioinformatics-based strategies as they apply specifically to lung cancer.

Transcriptomics, proteomics and metabolomics driven biomarker discovery in COPD: an update

INTRODUCTION

Diagnosis of chronic obstructive pulmonary disease (COPD), characterized by progressive irreversible airflow limitation, remains a challenge. Lack of sensitive diagnostic markers and alternative treatments have limited patients' survival rate. Herein, we provide for clinicians and scientists a comprehensive review on the various omics platforms used to investigate COPD.

AREAS COVERED

This review consists of articles from PubMed (2009-2016) as well as views of the contributing authors. The review highlights the need for COPD biomarker identification and also provides an update on promising candidate markers identified in various biological fluids using omics technologies. Expert commentary: The multi-omics approach holds promise for the development of robust early stage COPD diagnostic markers, screening of high-risk population, and also improved prognosis which could lead to personalized medicine in future. Various factors regulating an omics study including sample size, control selection, disease phenotyping, usage of complementary techniques and result replication in omics-based research are outlined.

Ultrastructural identification of telocytes in the muscularis of chicken ileum

Telocytes (TCs) are a specialized type of interstitial cells, characterized by a small cell body and long, thin processes, that have recently been identified in various cavitary and non-cavitary organs of humans and laboratory mammals. Chickens present significant economical and scientific notability; however, ultrastructural identification of TCs remains unclear in birds. The aim of the present study was to describe electron microscopic evidence for the presence of TCs in the chicken gut. The ileum of healthy adult broiler chickens (n=10) was studied by transmission electron microscopy. TCs are characterized by several, long (tens to hundreds of µm) prolongations called telopodes (Tps). Tps, which are below the resolving power of light microscopy, display podomeres (thin segments of ≤0.2 µm) and podoms (dilations accommodating caveolae, mitochondria and endoplasmic reticulum). TCs were observed in every field, but were predominantly located in the myenteric plexus and the lamina propria. Tps frequently establish close spatial relationships with immune cells, blood vessels and nerve endings. On the basis of their distribution and morphology, it was hypothesized that the different locations of TCs may be associated with different roles.

The potential of CXCL5 as a target for liver cancer - what do we know so far?

CXCL5, epithelial cell derived neutrophil attractant 78, is a CXC chemokine predominantly expressed on epithelial cells. It has specificity for CXCR2 receptors and is involved in the recruitment and activation of neutrophils. CXCL5 is considered a therapeutic target in liver cancer, since treatment with small-interfering RNAs or antibodies against CXCL5 can suppress tumor growth, proliferation, migration and invasion. Experimental evidence demonstrated that CXCL5 antibodies could reduce the tumor growth and synergistically increase the efficiency of the tyrosine kinase inhibitor, Gefitinib, without the addition of toxicity. A number of challenges are encountered and should be considered during the development and clinical application of CXCL5 target-specific drugs. The specificity of CXCL5 as a therapeutic target for certain types and duration of cancer should be more carefully clarified, since it seems that CXCL5 is involved in many molecular pathways and crosstalk between targeted chemokines/receptors. The concept that CXCL5 serves as the therapeutic target for liver cancer was evidenced by preclinical studies, and is the beginning of CXCL5-based drug discovery and development.

Dynamic gene expressions of peripheral blood mononuclear cells in patients with acute exacerbation of chronic obstructive pulmonary disease: a preliminary study

INTRODUCTION

Acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is a serious event that is responsible for the progress of the disease, increases in medical costs and high mortality.

METHODS

The aim of the present study was to identify AECOPD-specific biomarkers by evaluating the dynamic gene expression profiling of peripheral blood mononuclear cells (PBMCs) from patients with AECOPD on days 1, 3 and 10 after hospital admission and to compare the derived data with data from healthy controls or patients with stable COPD.

RESULTS

We found that 14 genes were co-differentially upregulated and 2 downregulated greater than 10-fold in patients with COPD or AECOPD compared with the healthy individuals. Eight co-differentially upregulated genes and six downregulated genes were identified as a panel of AECOPD-specific genes. Downregulation of TCF7 in PBMCs was found to be associated with the severity of COPD. Dynamic changes of Aminolevulinate-delta-synthase 2 and carbonic anhydrase I had similar patterns of Digital Evaluation Score System scores and may serve as potential genes of interest during the course of AECOPD.

CONCLUSION

Thus, our findings indicate a panel of altered gene expression patterns in PBMCs that can be used as AECOPD-specific dynamic biomarkers to monitor the course of AECOPD.

Gene polymorphisms and chronic obstructive pulmonary disease

The genetic component was suggested to contribute to the development of chronic obstructive pulmonary disease (COPD), a major and growing public health burden. The present review aims to characterize the evidence that gene polymorphisms contribute to the aetiology of COPD and related traits, and explore the potential relationship between certain gene polymorphisms and COPD susceptibility, severity, lung function, phenotypes, or drug effects, even though limited results from related studies lacked consistency. Most of these studies were association studies, rather than confirmatory studies. More large-sized and strictly controlled studies are needed to prove the relationship between gene polymorphisms and the reviewed traits. More importantly, prospective confirmatory studies beyond initial association studies will be necessary to evaluate true relationships between gene polymorphisms and COPD and help individualized treatment for patients with COPD.

Telocytes in the urinary system

BACKGROUND

Telocytes, a new type of interstitial cells, have been identified in many organs in mammals. The present studies aimed at investigating the ultrastructure, distribution and interactions of telocytes with surrounding cells in the urinary system of rats, to confirm the existence of telocytes in kidneys, ureter and urinary bladder.

METHODS

Samples of kidney, ureter, or urinary bladder were harvested for the ultrastructure by the electron microscope. The primary culture of telocytes was performed to investigate the dynamic alterations.

RESULTS

Telocytes mainly located in the sub-capsular space of kidney, or between smooth muscle bundles and in the lamina propria of ureter and urinary bladder. Telocytes established numerous contacts with macrophages in the sub-capsular space of kidney, or with smooth muscle cells, nerve endings as well as blood capillaries in the ureter and urinary bladder. The complete morphology of telocytes with telopodes was observed clearly through the primary cell culture from the kidney tissues of rats.

CONCLUSIONS

Our data evidenced the existence of telocytes in the urinary system, which may contribute to the tissue reparation and regeneration.

Genetic network and gene set enrichment analysis to identify biomarkers related to cigarette smoking and lung cancer

OBJECTIVES

Cigarette smoking is the most demonstrated risk factor for the development of lung cancer, while the related genetic mechanisms are still unclear.

METHODS

The preprocessed microarray expression dataset was downloaded from Gene Expression Omnibus database. Samples were classified according to the disease state, stage and smoking state. A new computational strategy was applied for the identification and biological interpretation of new candidate genes in lung cancer and smoking by coupling a network-based approach with gene set enrichment analysis.

MEASUREMENTS

Network analysis was performed by pair-wise comparison according to the disease states (tumor or normal), smoking states (current smokers or nonsmokers or former smokers), or the disease stage (stages I-IV). The most activated metabolic pathways were identified by gene set enrichment analysis.

RESULTS

Panels of top ranked gene candidates in smoking or cancer development were identified, including genes involved in cell proliferation and drug metabolism like cytochrome P450 and WW domain containing transcription regulator 1. Semaphorin 5A and protein phosphatase 1F are the common genes represented as major hubs in both the smoking and cancer related network. Six pathways, e.g. cell cycle, DNA replication, RNA transport, protein processing in endoplasmic reticulum, vascular smooth muscle contraction and endocytosis were commonly involved in smoking and lung cancer when comparing the top ten selected pathways.

CONCLUSION

New approach of bioinformatics for biomarker identification and validation can probe into deep genetic relationships between cigarette smoking and lung cancer. Our studies indicate that disease-specific network biomarkers, interaction between genes/proteins, or cross-talking of pathways provide more specific values for the development of precision therapies for lung.