scholarly journals PulmonDB: a curated lung disease gene expression database

2019 ◽  
Author(s):  
Ana B. Villaseñor-Altamirano ◽  
Marco Moretto ◽  
Alejandra Zayas-Del Moral ◽  
Mariel Maldonado ◽  
Adrián Munguía-Reyes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Disease Gene ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Chronic Obstructive ◽  
Obstructive Pulmonary Disease ◽  
Web Based ◽  
Public Repositories ◽  
New Hypothesis ◽  
Different Sources

ABSTRACTChronic Obstructive Pulmonary Disease (COPD) and Idiopathic Pulmonary Fibrosis (IPF) have contrasting clinical and pathological characteristics, and interesting whole-genome transcriptomic profiles. However, data from public repositories are difficult to reprocess and reanalyze. Here we present PulmonDB, a web-based database (http://pulmondb.liigh.unam.mx/) and R library that facilitates exploration of gene expression profiles for these diseases by integrating transcriptomic data and curated annotation from different sources. We demonstrated the value of this resource by presenting the expression of already well-known genes of COPD and IPF across multiple experiments and the results of two differential expression analyses in which we successfully identified differences and similarities. With this first version of PulmonDB, we create a new hypothesis and compare the two diseases from a transcriptomics perspective.

scholarly journals Age and Alzheimer’s disease gene expression profiles reversed by the glutamate modulator riluzole

2016 ◽  
Vol 22 (2) ◽  
pp. 296-305 ◽  
Author(s):  
A C Pereira ◽  
J D Gray ◽  
J F Kogan ◽  
R L Davidson ◽  
T G Rubin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Disease Gene ◽  
Expression Profiles ◽  
Gene Expression Profiles

scholarly journals Pulmonary neuroendocrine cells: physiology, tissue homeostasis and disease

2020 ◽  
Vol 13 (12) ◽  
pp. dmm046920
Author(s):  
Masafumi Noguchi ◽  
Kana T. Furukawa ◽  
Mitsuru Morimoto
Keyword(s):  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Lung Ventilation ◽  
Neuroendocrine Cells ◽  
Chronic Obstructive ◽  
Obstructive Pulmonary Disease ◽  
Congenital Diseases ◽  
Hypoxic Conditions ◽  
Pulmonary Neuroendocrine Cells ◽  
Large Clusters

ABSTRACTMammalian lungs have the ability to recognize external environments by sensing different compounds in inhaled air. Pulmonary neuroendocrine cells (PNECs) are rare, multi-functional epithelial cells currently garnering attention as intrapulmonary sensors; PNECs can detect hypoxic conditions through chemoreception. Because PNEC overactivation has been reported in patients suffering from respiratory diseases – such as asthma, chronic obstructive pulmonary disease, bronchopulmonary dysplasia and other congenital diseases – an improved understanding of the fundamental characteristics of PNECs is becoming crucial in pulmonary biology and pathology. During the past decade, murine genetics and disease models revealed the involvement of PNECs in lung ventilation dynamics, mechanosensing and the type 2 immune responses. Single-cell RNA sequencing further unveiled heterogeneous gene expression profiles in the PNEC population and revealed that a small number of PNECs undergo reprogramming during regeneration. Aberrant large clusters of PNECs have been observed in neuroendocrine tumors, including small-cell lung cancer (SCLC). Modern innovation of imaging analyses has enabled the discovery of dynamic migratory behaviors of PNECs during airway development, perhaps relating to SCLC malignancy. This Review summarizes the findings from research on PNECs, along with novel knowledge about their function. In addition, it thoroughly addresses the relevant questions concerning the molecular pathology of pulmonary diseases and related therapeutic approaches.

scholarly journals Abundance of Non-Polarized Lung Macrophages with Poor Phagocytic Function in Chronic Obstructive Pulmonary Disease (COPD)

Biomedicines ◽  
2020 ◽  
Vol 8 (10) ◽  
pp. 398
Author(s):  
Kentaro Akata ◽  
Kei Yamasaki ◽  
Fernando Sergio Leitao Filho ◽  
Chen Xi Yang ◽  
Hiroto Takiguchi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chronic Obstructive Pulmonary Disease ◽  
Bronchoalveolar Lavage ◽  
Pulmonary Disease ◽  
Expression Profiles ◽  
Chronic Obstructive ◽  
Phagocytic Function ◽  
Pathogen Recognition ◽  
Obstructive Pulmonary Disease ◽  
Lung Macrophages

Lung macrophages are the key immune effector cells in the pathogenesis of Chronic Obstructive Pulmonary Disease (COPD). Several studies have shown an increase in their numbers in bronchoalveolar lavage fluid (BAL) of subjects with COPD compared to controls, suggesting a pathogenic role in disease initiation and progression. Although reduced lung macrophage phagocytic ability has been previously shown in COPD, the relationship between lung macrophages’ phenotypic characteristics and functional properties in COPD is still unclear. (1) Methods: Macrophages harvested from bronchoalveolar lavage (BAL) fluid of subjects with and without COPD (GOLD grades, I–III) were immuno-phenotyped, and their function and gene expression profiles were assessed using targeted assays. (2) Results: BAL macrophages from 18 COPD and 10 (non-COPD) control subjects were evaluated. The majority of macrophages from COPD subjects were non-polarized (negative for both M1 and M2 markers; 77.9%) in contrast to controls (23.9%; p < 0.001). The percentages of these non-polarized macrophages strongly correlated with the severity of COPD (p = 0.006) and current smoking status (p = 0.008). Non-polarized macrophages demonstrated poor phagocytic function in both the control (p = 0.02) and COPD (p < 0.001) subjects. Non-polarized macrophages demonstrated impaired ability to phagocytose Staphylococcus aureus (p < 0.001). They also demonstrated reduced gene expression for CD163, CD40, CCL13 and C1QA&B, which are involved in pathogen recognition and processing and showed an increased gene expression for CXCR4, RAF1, amphiregulin and MAP3K5, which are all involved in promoting the inflammatory response. (3) Conclusions: COPD is associated with an abundance of non-polarized airway macrophages that is related to the severity of COPD. These non-polarized macrophages are predominantly responsible for the poor phagocytic capacity of lung macrophages in COPD, having reduced capacity for pathogen recognition and processing. This could be a key risk factor for COPD exacerbation and could contribute to disease progression.

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