Towards a functional proteomics approach to the comprehension of idiopathic pulmonary fibrosis, sarcoidosis, systemic sclerosis and pulmonary Langerhans cell histiocytosis

Landi, Claudia; Bargagli, Elena; Bianchi, Laura; Gagliardi, Assunta; Carleo, Alfonso; Bennett, David; Perari, M. G.; Armini, Alessandro; Prasse, Antje; Rottoli, Paola; Bini, Luca

doi:10.1016/j.jprot.2013.03.006

Cited by 55 publications

(46 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…These types of in silico analysis include annotated databases and metabolic and signaling pathways gathered from publications. Protein names were manually inserted in the system and all interactions processed considering canonical paths (Landiet al, ).…”

Section: Methodsmentioning

confidence: 99%

Gene and protein expression in the reproductive tract of Brazilian Somalis rams

Bezerra

Silva

Lobo

et al. 2019

Reprod Domestic Animals

View full text Add to dashboard Cite

Contents Brazilian Somalis is a locally‐adapted breed of rams raised in tropical climate and native pastures. The present study was conducted to evaluate gene expression and proteome of the reproductive tract of such rams. Samples were collected from testes, epididymides, seminal vesicles and bulbourethral glands of four rams. Expression of clusterin (CLU), osteopontin (OPN) and prostaglandin D2 synthase (PGDS) genes were evaluated in all samples by real‐time PCR. Shotgun proteomic analysis was performed using samples from the head, corpus and cauda epididymides and from all other structures as well. Gene ontology terms and protein interactions were obtained from UniProtKB databases and MetaCore v.6.8 platform. CLU trasncripts were detected in the testes, epididymides, seminal vesicles and bulbourethral glands of the Somalis rams. The initial region and body of the epididymis had the greatest CLU expression. OPN mRNA was localized in all tissues of the ram reproductive tract. PGDS mRNA was detected in the testes and epididymides. Lable‐free mass spectrometry allowed the identification of 137 proteins in all samples. Proteins of the epididymis head mainly participate in cellular processes and response to stimulus, participating in catalityc activity and binding. Proteins of epididymis body acted as regulatory proteins and in cellular processes, with binding and catalytic activity. Cauda epididymis molecules were associated with cellular processes and regulation, with binding function and catalytic activity as well. Testis proteins were mainly linked to cell processes and response to stimuli, and had catalytic function. Seminal vesicle proteins were involved in regulation and mainly with binding functions. Most bulbourethral gland proteins participated in cellular processes. The present study is the first to evaluate the proteome and gene expressions in the reproductive tract of Brazilian Somalis rams. Such pieces of information bring significant cointribution for the understanding of the reproductive physiology of locally‐adapted livestock.

show abstract

Section: Methodsmentioning

confidence: 99%

Gene and protein expression in the reproductive tract of Brazilian Somalis rams

Bezerra

Silva

Lobo

et al. 2019

Reprod Domestic Animals

View full text Add to dashboard Cite

show abstract

“…There are multiple technologies and methods for peptide fractionation, enrichment, ionization and types of mass spectrometers commercially available . MS has been used widely in biomarker studies of respiratory disease to date including chronic obstructive pulmonary disease (COPD), acute respiratory distress syndrome (ARDS) and interstitial lung disease (ILD) …”

Section: Proteomic Applications and Challengesmentioning

confidence: 99%

Proteomics: Clinical and research applications in respiratory diseases

et al. 2018

View full text Add to dashboard Cite

The proteome is the study of the protein content of a definable component of an organism in biology. However, the tissue-specific expression of proteins and the varied post-translational modifications, splice variants and protein-protein complexes that may form, make the study of protein a challenging yet vital tool in answering many of the unanswered questions in medicine and biology to date. Indeed, the spatial, temporal and functional composition of proteins in the human body has proven difficult to elucidate for many years. Given the effect of microRNA and epigenetic regulation on silencing and enhancing gene transcription, the study of protein arguably provides more accurate information on homeostasis and perturbation in health and disease. There have been significant advances in the field of proteomics in recent years, with new technologies and platforms available to the research community. In this review, we briefly discuss some of these new technologies and developments in the context of respiratory disease. We also discuss the types of data science approaches to analyses and interpretation of the large volumes of data generated in proteomic studies. We discuss the application of these technologies with regard to respiratory disease and highlight the potential for proteomics in generating major advances in the understanding of respiratory pathophysiology into the future.

show abstract

“…Protein profiles specific to Ventilator-associated pneumonia (VAP) were readily identified in BALF, offering promising candidates for understanding the mechanism driving VAP [142]. Likewise, protein signatures of sarcoidosis, IPF, pulmonary langerhans cell histiocytosis, PF due to systemic sclerosis were highlighted, and using systems biology platforms, common and distinct pathways were identified [143]. Intriguingly, phosphoproteomics on lung tissues of lung cancer and COPD patients revealed that activation of the NF-κB pathway was the most relevant signaling link between the two diseases, providing clues to developing therapies [144–148].…”

Section: Proteomics and Metabolomics In Pulmonary Biologymentioning

confidence: 99%

Integrating <b><i>Omics</i></b> Technologies to Study Pulmonary Physiology and Pathology at the Systems Level

Pathak¹,

Davé

2014

Cell Physiol Biochem

View full text Add to dashboard Cite

Assimilation and integration of “omics” technologies, including genomics, epigenomics, proteomics, and metabolomics has readily altered the landscape of medical research in the last decade. The vast and complex nature of omics data can only be interpreted by linking molecular information at the organismic level, forming the foundation of systems biology. Research in pulmonary biology/medicine has necessitated integration of omics, network, systems and computational biology data to differentially diagnose, interpret, and prognosticate pulmonary diseases, facilitating improvement in therapy and treatment modalities. This review describes how to leverage this emerging technology in understanding pulmonary diseases at the systems level -called a “systomic” approach. Considering the operational wholeness of cellular and organ systems, diseased genome, proteome, and the metabolome needs to be conceptualized at the systems level to understand disease pathogenesis and progression. Currently available omics technology and resources require a certain degree of training and proficiency in addition to dedicated hardware and applications, making them relatively less user friendly for the pulmonary biologist and clinicians. Herein, we discuss the various strategies, computational tools and approaches required to study pulmonary diseases at the systems level for biomedical scientists and clinical researchers.

show abstract

Towards a functional proteomics approach to the comprehension of idiopathic pulmonary fibrosis, sarcoidosis, systemic sclerosis and pulmonary Langerhans cell histiocytosis

Cited by 55 publications

References 49 publications

Gene and protein expression in the reproductive tract of Brazilian Somalis rams

Gene and protein expression in the reproductive tract of Brazilian Somalis rams

Proteomics: Clinical and research applications in respiratory diseases

Integrating <b><i>Omics</i></b> Technologies to Study Pulmonary Physiology and Pathology at the Systems Level

Contact Info

Product

Resources

About