Cystic Fibrosis: Systems Biology Analysis from Homozygous p.Phe508del Variant Patients’ Samples Reveals Perturbations in Tissue-Specific Pathways

Cystic fibrosis (CF) is an autosomal recessive disorder, caused by diverse genetic variants for the CF transmembrane conductance regulator (CFTR) protein. Among these, p.Phe508del is the most prevalent variant. The effects of this variant on the physiology of each tissue remains unknown. This study is aimed at predicting cell signaling pathways present in different tissues of fibrocystic patients, homozygous for p.Phe508del. The study involved analysis of two microarray datasets, E-GEOD-15568 and E-MTAB-360 corresponding to the rectal and bronchial epithelium, respectively, obtained from the ArrayExpress repository. Particularly, differentially expressed genes (DEGs) were predicted, protein-protein interaction (PPI) networks were designed, and centrality and functional interaction networks were analyzed. The study reported that p.Phe508del-mutated CFTR-allele in homozygous state influenced the whole gene expression in each tissue differently. Interestingly, gene ontology (GO) term enrichment analysis revealed that only “neutrophil activation” was shared between both tissues; however, nonshared DEGs were grouped into the same GO term. For further verification, functional interaction networks were generated, wherein no shared nodes were reported between these tissues. These results suggested that the p.Phe508del-mutated CFTR-allele in homozygous state promoted tissue-specific pathways in fibrocystic patients. The generated data might further assist in prediction diagnosis to define biomarkers or devising therapeutic strategies.

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Serum-Based Proteomics Profiling in Adult Patients with Cystic Fibrosis

International Journal of Molecular Sciences ◽

10.3390/ijms21197415 ◽

2020 ◽

Vol 21 (19) ◽

pp. 7415

Author(s):

Hicham Benabdelkamel ◽

Hanadi Alamri ◽

Meshail Okla ◽

Afshan Masood ◽

Mai Abdel Jabar ◽

...

Keyword(s):

Cystic Fibrosis ◽

Multiple Reaction Monitoring ◽

Autosomal Recessive Disorder ◽

Mass Spectrometry Analysis ◽

Spectrometry Analysis ◽

Serum Proteomics ◽

Proteomic Approach ◽

Significant Difference ◽

Canonical Pathways ◽

Cf Transmembrane Conductance Regulator

Cystic fibrosis (CF), the most common lethal autosomal recessive disorder among Caucasians, is caused by mutations in the CF transmembrane conductance regulator (CFTR) chloride channel gene. Despite significant advances in the management of CF patients, novel disease-related biomarkers and therapies must be identified. We performed serum proteomics profiling in CF patients (n = 28) and healthy subjects (n = 10) using the 2D-DIGE MALDI-TOF proteomic approach. Out of a total of 198 proteins identified, 134 showed a statistically significant difference in abundance and a 1.5-fold change (ANOVA, p < 0.05), including 80 proteins with increased abundance and 54 proteins with decreased abundance in CF patients. A multiple reaction monitoring-mass spectrometry analysis of six differentially expressed proteins identified by a proteomic approach (DIGE-MALD-MS) showed a significant increase in C3 and CP proteins and a decrease in APOA1, Complement C1, Hp, and RBP4proteins compared with healthy controls. Fifteen proteins were identified as potential biomarkers for CF diagnosis. An ingenuity pathway analysis of the differentially regulated proteins indicates that the central nodes dysregulated in CF subjects involve pro-inflammatory cytokines, ERK1/2, and P38 MAPK, which are primarily involved in catalytic activities and metabolic processes. The involved canonical pathways include those related to FXR/RXR, LXR/RXR, acute phase response, IL12, nitric oxide, and reactive oxygen species in macrophages. Our data support the current efforts toward augmenting protease inhibitors in patients with CF. Perturbations in lipid and vitamin metabolism frequently observed in CF patients may be partly due to abnormalities in their transport mechanism.

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Antisense oligonucleotide-mediated correction of CFTR splicing improves chloride secretion in cystic fibrosis patient-derived bronchial epithelial cells

Nucleic Acids Research ◽

10.1093/nar/gkaa490 ◽

2020 ◽

Author(s):

Wren E Michaels ◽

Robert J Bridges ◽

Michelle L Hastings

Keyword(s):

Cystic Fibrosis ◽

Membrane Conductance ◽

Anion Channel ◽

Autosomal Recessive Disorder ◽

Premature Termination Codon ◽

Chloride Secretion ◽

Aberrant Splicing ◽

Bronchial Epithelial ◽

Cryptic Exon ◽

Cf Transmembrane Conductance Regulator

Abstract Cystic fibrosis (CF) is an autosomal recessive disorder caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, encoding an anion channel that conducts chloride and bicarbonate across epithelial membranes. Mutations that disrupt pre-mRNA splicing occur in >15% of CF cases. One common CFTR splicing mutation is CFTR c.3718-2477C>T (3849+10 kb C>T), which creates a new 5′ splice site, resulting in splicing to a cryptic exon with a premature termination codon. Splice-switching antisense oligonucleotides (ASOs) have emerged as an effective therapeutic strategy to block aberrant splicing. We test an ASO targeting the CFTR c.3718-2477C>T mutation and show that it effectively blocks aberrant splicing in primary bronchial epithelial (hBE) cells from CF patients with the mutation. ASO treatment results in long-term improvement in CFTR activity in hBE cells, as demonstrated by a recovery of chloride secretion and apical membrane conductance. We also show that the ASO is more effective at recovering chloride secretion in our assay than ivacaftor, the potentiator treatment currently available to these patients. Our findings demonstrate the utility of ASOs in correcting CFTR expression and channel activity in a manner expected to be therapeutic in patients.

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Impact of the different mutations in the cystic fibrosis gene in children with chronic rhinosinusitis

Journal of Otolaryngology-ENT Research ◽

10.15406/joentr.2019.11.00437 ◽

2019 ◽

Vol 11 (5) ◽

pp. 211-214

Author(s):

Mafalda da Silva Ferreira ◽

João Elói Moura ◽

Ana Margarida Amorim ◽

Ana Bernardo Ferreira ◽

Luís Filipe Silva

Keyword(s):

Cystic Fibrosis ◽

Chronic Rhinosinusitis ◽

Upper Airway ◽

Autosomal Recessive Disorder ◽

The Body ◽

University Hospital ◽

Cystic Fibrosis Gene ◽

Lower Airway ◽

Persistent Symptoms ◽

Cf Transmembrane Conductance Regulator

Background: Cystic fibrosis (CF) is a worldwide disease occurring mostly in caucasians. It is an autosomal recessive disorder that leads to a malfunction of CF transmembrane conductance regulator (CFTR). These mutations cause an ionic disorder on the body fluids and a modification on its consistency. Affects multiple parts of the body and rhinosinusitis is a common manifestation of the upper airway affection. Material and methods: This retrospective study performed a statistical analysis of the prevelence of chronic rhinosinusitis with polyposis, genotipe and mortality in 30 children under 18 years with cystic fibrosis followed in the CF unit of Coimbra University Hospital. Results: The mean age of this study was 12,9 years. Phenylalanine deletion at position 508 (F508delF508del) was the most prevalent genotype (66,7%). Females patients had an higher prevalence of morbidities, however male patients had an higher mortality rate 20% comparing to 6,7%. Nasal polyposis was present only in the living ones with F508delF508del genotype. ENT (ear, nouse and throut) symptons and an abnormal ENT examination were mostly observed in F508delF508del genotype. Conclusions: CF is a lifelong disease that requires long-term surveillance and compliance. The involvement of the lower airway is prevalent in young chlidren. The uper airway symptoms becomes more important with disease progression. Nasal poliposis is prevalent on the older ones with F508delF508del genotype. In this kind of patients with persistent symptoms, who have failed medical management, are often considered appropriate candidates for functional endoscopic surgery.

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Identification of COVID-19 and Dengue Host Factor Interaction Networks Based on Integrative Bioinformatics Analyses

Frontiers in Immunology ◽

10.3389/fimmu.2021.707287 ◽

2021 ◽

Vol 12 ◽

Author(s):

Wenjiang Zheng ◽

Hui Wu ◽

Chengxin Liu ◽

Qian Yan ◽

Ting Wang ◽

...

Keyword(s):

Signaling Pathways ◽

Treatment Options ◽

Enrichment Analysis ◽

Host Factor ◽

Interaction Networks ◽

Biological Functions ◽

Bioinformatics Analyses ◽

Health Crisis ◽

Tissue Specific ◽

Factor Interaction

BackgroundThe outbreak of Coronavirus disease 2019 (COVID-19) has become an international public health crisis, and the number of cases with dengue co-infection has raised concerns. Unfortunately, treatment options are currently limited or even unavailable. Thus, the aim of our study was to explore the underlying mechanisms and identify potential therapeutic targets for co-infection.MethodsTo further understand the mechanisms underlying co-infection, we used a series of bioinformatics analyses to build host factor interaction networks and elucidate biological process and molecular function categories, pathway activity, tissue-specific enrichment, and potential therapeutic agents.ResultsWe explored the pathologic mechanisms of COVID-19 and dengue co-infection, including predisposing genes, significant pathways, biological functions, and possible drugs for intervention. In total, 460 shared host factors were collected; among them, CCL4 and AhR targets were important. To further analyze biological functions, we created a protein-protein interaction (PPI) network and performed Molecular Complex Detection (MCODE) analysis. In addition, common signaling pathways were acquired, and the toll-like receptor and NOD-like receptor signaling pathways exerted a significant effect on the interaction. Upregulated genes were identified based on the activity score of dysregulated genes, such as IL-1, Hippo, and TNF-α. We also conducted tissue-specific enrichment analysis and found ICAM-1 and CCL2 to be highly expressed in the lung. Finally, candidate drugs were screened, including resveratrol, genistein, and dexamethasone.ConclusionsThis study probes host factor interaction networks for COVID-19 and dengue and provides potential drugs for clinical practice. Although the findings need to be verified, they contribute to the treatment of co-infection and the management of respiratory disease.

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Antisense oligonucleotide-mediated correction of CFTR splicing improves chloride secretion in cystic fibrosis patient-derived bronchial epithelial cells

10.1101/2020.05.12.089417 ◽

2020 ◽

Author(s):

Wren E. Michaels ◽

Robert J. Bridges ◽

Michelle L. Hastings

Keyword(s):

Cystic Fibrosis ◽

Membrane Conductance ◽

Anion Channel ◽

Autosomal Recessive Disorder ◽

Premature Termination Codon ◽

Chloride Secretion ◽

Aberrant Splicing ◽

Bronchial Epithelial ◽

Cryptic Exon ◽

Cf Transmembrane Conductance Regulator

ABSTRACTCystic fibrosis (CF) is an autosomal recessive disorder caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, encoding an anion channel that conducts chloride and bicarbonate across epithelial membranes. Mutations that disrupt pre-mRNA splicing occur in more than 15% of CF cases. One common CFTR splicing mutation is CFTR c.3718-2477C>T (3849+10kbC>T), which creates a new 5’ splice site, resulting in splicing to a cryptic exon with a premature termination codon. Splice-switching antisense oligonucleotides (ASOs) have emerged as an effective therapeutic strategy to block aberrant splicing. We test an ASO targeting the CFTR c.3718-2477C>T mutation and show that it effectively blocks aberrant splicing in primary bronchial epithelial (hBE) cells from CF patients with the mutation. ASO treatment results in long-term improvement in CFTR activity in hBE cells, as demonstrated by a recovery of chloride secretion and apical membrane conductance. We also show that the ASO is more effective at recovering chloride secretion in our assay than ivacaftor, the potentiator treatment currently available to these patients. Our findings demonstrate the utility of ASOs in correcting CFTR expression and channel activity in a manner expected to be therapeutic in patients.

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WEADE: A Workflow for Enrichment Analysis and Data Exploration

10.1101/252924 ◽

2018 ◽

Cited By ~ 1

Author(s):

Nils Trost ◽

Eugen Rempel ◽

Olga Ermakova ◽

Srividya Tamirisa ◽

Letiția Pârcălăbescu ◽

...

Keyword(s):

Web Application ◽

Graphical Representation ◽

Enrichment Analysis ◽

Interaction Networks ◽

Expression Data ◽

Functional Interaction ◽

Output Data ◽

Large Gene ◽

Web Tools ◽

Consistent Manner

ABSTRACTData analysis based on enrichment of Gene Ontology terms has become an important step in exploring large gene or protein expression datasets and several stand-alone or web tools exist for that purpose. However, a comprehensive and consistent analysis downstream of the enrichment calculation is missing so far. With WEADE we present a free web application that offers an integrated workflow for the exploration of genomic data combining enrichment analysis with a versatile set of tools to directly compare and intersect experiments or candidate gene lists of any size or origin including cross-species data. Lastly, WEADE supports the graphical representation of output data in the form of functional interaction networks based on prior knowledge, allowing users to go from plain expression data to functionally relevant candidate sub-lists in an interactive and consistent manner.

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Differential global gene expression in cystic fibrosis nasal and bronchial epithelium

Genomics ◽

10.1016/j.ygeno.2011.06.008 ◽

2011 ◽

Vol 98 (5) ◽

pp. 327-336 ◽

Cited By ~ 38

Author(s):

Varrie Ogilvie ◽

Margaret Passmore ◽

Laura Hyndman ◽

Lisa Jones ◽

Barbara Stevenson ◽

...

Keyword(s):

Gene Expression ◽

Cystic Fibrosis ◽

Bronchial Epithelium ◽

Global Gene Expression

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14-3-3 phosphoprotein interaction networks – does isoform diversity present functional interaction specification?

Frontiers in Plant Science ◽

10.3389/fpls.2012.00190 ◽

2012 ◽

Vol 3 ◽

Cited By ~ 50

Author(s):

Anna-Lisa Paul ◽

Fiona C. Denison ◽

Eric R. Schultz ◽

Agata K. Zupanska ◽

Robert J. Ferl

Keyword(s):

Interaction Networks ◽

Functional Interaction ◽

Isoform Diversity

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Identification of Key Genes and miRNAs in Osteosarcoma Patients with Chemoresistance by Bioinformatics Analysis

BioMed Research International ◽

10.1155/2018/4761064 ◽

2018 ◽

Vol 2018 ◽

pp. 1-10 ◽

Cited By ~ 9

Author(s):

Binbin Xie ◽

Yiran Li ◽

Rongjie Zhao ◽

Yuzi Xu ◽

Yuhui Wu ◽

...

Keyword(s):

Enrichment Analysis ◽

Gene Expression Omnibus ◽

Differentially Expressed ◽

Pathway Enrichment Analysis ◽

Regulation Of Transcription ◽

Functional Annotations ◽

Protein Protein Interaction ◽

Ppi Networks ◽

Search Tool ◽

Poor Outcomes

Chemoresistance is a significant factor associated with poor outcomes of osteosarcoma patients. The present study aims to identify Chemoresistance-regulated gene signatures and microRNAs (miRNAs) in Gene Expression Omnibus (GEO) database. The results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) included positive regulation of transcription, DNA-templated, tryptophan metabolism, and the like. Then differentially expressed genes (DEGs) were uploaded to Search Tool for the Retrieval of Interacting Genes (STRING) to construct protein-protein interaction (PPI) networks, and 9 hub genes were screened, such as fucosyltransferase 3 (Lewis blood group) (FUT3) whose expression in chemoresistant samples was high, but with a better prognosis in osteosarcoma patients. Furthermore, the connection between DEGs and differentially expressed miRNAs (DEMs) was explored. GEO2R was utilized to screen out DEGs and DEMs. A total of 668 DEGs and 5 DEMs were extracted from GSE7437 and GSE30934 differentiating samples of poor and good chemotherapy reaction patients. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used to perform GO and KEGG pathway enrichment analysis to identify potential pathways and functional annotations linked with osteosarcoma chemoresistance. The present study may provide a deeper understanding about regulatory genes of osteosarcoma chemoresistance and identify potential therapeutic targets for osteosarcoma.

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