Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease

Thomas, John P.; Módos, Dezső; Korcsmáros, Tamás; Brooks-Warburton, Johanne

doi:10.3389/fgene.2021.760501

Cited by 14 publications

(12 citation statements)

References 134 publications

(166 reference statements)

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“…It is expected that the multi-omics method may be more robust in guiding the precise treatment of IBD and other complex diseases ( 71 , 72 ). With the exponential increase in the availability of molecular data utilized through omics technology, network biology could become a valuable tool for analyzing patient data from multiple omics to achieve the key goals of PM for IBD and other complex diseases ( 73 , 74 ). In addition, artificial intelligence, including machine learning and deep learning, could provide many potential solutions for the treatment of IBD ( 75 ).…”

Section: Discussionmentioning

confidence: 99%

Research hotspot and trend analysis in the diagnosis of inflammatory bowel disease: A machine learning bibliometric analysis from 2012 to 2021

Liu

Zhang

et al. 2022

Front. Immunol.

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AimsThis study aimed to conduct a bibliometric analysis of the relevant literature on the diagnosis of inflammatory bowel disease (IBD), and show its current status, hot spots, and development trends.MethodsThe literature on IBD diagnosis was acquired from the Science Citation Index Expanded of the Web of Science Core Collection. Co-occurrence and cooperation relationship analysis of authors, institutions, countries, journals, references, and keywords in the literature were carried out through CiteSpace software and the Online Analysis platform of Literature Metrology. At the same time, the relevant knowledge maps were drawn, and the keywords cluster analysis and emergence analysis were performed.Results14,742 related articles were included, showing that the number of articles in this field has increased in recent years. The results showed that PEYRIN-BIROULET L from the University Hospital of Nancy-Brabois was the author with the most cumulative number of articles. The institution with the most articles was Mayo Clin, and the United States was far ahead in the article output and had a dominant role. Keywords analysis showed that there was a total of 818 keywords, which were mainly focused on the research of related diseases caused or coexisted by IBD, such as colorectal cancer and autoimmune diseases, and the diagnosis and treatment methods of IBD. Emerging analysis showed that future research hotspots and trends might be the treatment of IBD and precision medicine.ConclusionThis research was the first bibliometric analysis of publications in the field of IBD diagnosis using visualization software and data information mining, and obtained the current status, hotspots, and development of this field. The future research hotspot might be the precision medicine of IBD, and the mechanism needed to be explored in depth to provide a theoretical basis for its clinical application.

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Section: Discussionmentioning

confidence: 99%

Research hotspot and trend analysis in the diagnosis of inflammatory bowel disease: A machine learning bibliometric analysis from 2012 to 2021

Liu

Zhang

et al. 2022

Front. Immunol.

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“…To enhance transparency and accessibility of bio-sample data, standardization and harmonization of data frameworks are needed at a global level. A Data Commons should be established to facilitate global collaboration and provide access to biospecimens and data before and after treatment with established and novel therapies[ 3 , 51 ].…”

Section: Precision Medicine To Predict Disease Susceptibility Diagnos...mentioning

confidence: 99%

“…The pathophysiology of ulcerative colitis (UC) and Crohn’s disease (CD) is increasingly evolving, mainly focusing on its genome, exposome, microbiome, immunome, and many other omics approaches. Thomas et al [ 3 ] noted that the development of IBD is attributed to an aberrant immune reaction resulting from intricate interactions among various genetic risk factors, imbalanced gut flora, and environmental influences. Unlike rare and clearly defined monogenic disorders, IBD arises from mutations in multiple genes rather than a single gene[ 3 ].…”

Section: Introductionmentioning

confidence: 99%

“…Thomas et al [ 3 ] noted that the development of IBD is attributed to an aberrant immune reaction resulting from intricate interactions among various genetic risk factors, imbalanced gut flora, and environmental influences. Unlike rare and clearly defined monogenic disorders, IBD arises from mutations in multiple genes rather than a single gene[ 3 ]. In this sense, precision medicine is pivotal in creating personalized therapies combining these various aspects into a multiomics approach[ 4 ].…”

Section: Introductionmentioning

confidence: 99%

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Integration and implementation of precision medicine in the multifaceted inflammatory bowel disease

Jagirdhar,

Perez,

Perez

et al. 2023

World J Gastroenterol

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The liver is one of the organs most commonly involved in metastatic disease, especially due to its unique vascularization. It’s well known that liver metastases represent the most common hepatic malignant tumors. From a practical point of view, it’s of utmost importance to evaluate the presence of liver metastases when staging oncologic patients, to select the best treatment possible, and finally to predict the overall prognosis. In the past few years, imaging techniques have gained a central role in identifying liver metastases, thanks to ultrasonography, contrast-enhanced computed tomography (CT), and magnetic resonance imaging (MRI). All these techniques, especially CT and MRI, can be considered the non-invasive reference standard techniques for the assessment of liver involvement by metastases. On the other hand, the liver can be affected by different focal lesions, sometimes benign, and sometimes malignant. On these bases, radiologists should face the differential diagnosis between benign and secondary lesions to correctly allocate patients to the best management. Considering the above-mentioned principles, it’s extremely important to underline and refresh the broad spectrum of liver metastases features that can occur in everyday clinical practice. This review aims to summarize the most common imaging features of liver metastases, with a special focus on typical and atypical appearance, by using MRI.

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“…With the exponential increase in the availability of disease-specific gene expression data, especially in complex diseases such as IBD [ 25 ], there are new opportunities to further investigate the role of miRNAs in disease pathogenesis. In the following section, we provide a technical summary describing the steps required to perform transcriptome-based miRNA-target gene analysis in complex disorders.…”

Section: Bioinformatics Approaches For Predicting Mirna Function In C...mentioning

confidence: 99%

Analysing miRNA-Target Gene Networks in Inflammatory Bowel Disease and Other Complex Diseases Using Transcriptomic Data

Thomas

Ölbei

Brooks-Warburton

et al. 2022

Genes

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Patients with inflammatory bowel disease (IBD) are known to have perturbations in microRNA (miRNA) levels as well as altered miRNA regulation. Although experimental methods have provided initial insights into the functional consequences that may arise due to these changes, researchers are increasingly utilising novel bioinformatics approaches to further dissect the role of miRNAs in IBD. The recent exponential increase in transcriptomics datasets provides an excellent opportunity to further explore the role of miRNAs in IBD pathogenesis. To effectively understand miRNA-target gene interactions from gene expression data, multiple database resources are required, which have become available in recent years. In this technical note, we provide a step-by-step protocol for utilising these state-of-the-art resources, as well as systems biology approaches to understand the role of miRNAs in complex disease pathogenesis. We demonstrate through a case study example how to combine the resulting miRNA-target gene networks with transcriptomics data to find potential disease-specific miRNA regulators and miRNA-target genes in Crohn’s disease. This approach could help to identify miRNAs that may have important disease-modifying effects in IBD and other complex disorders, and facilitate the discovery of novel therapeutic targets.

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Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease

Cited by 14 publications

References 134 publications

Research hotspot and trend analysis in the diagnosis of inflammatory bowel disease: A machine learning bibliometric analysis from 2012 to 2021

Research hotspot and trend analysis in the diagnosis of inflammatory bowel disease: A machine learning bibliometric analysis from 2012 to 2021

Integration and implementation of precision medicine in the multifaceted inflammatory bowel disease

Analysing miRNA-Target Gene Networks in Inflammatory Bowel Disease and Other Complex Diseases Using Transcriptomic Data

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