Next-generation sequencing in the diagnosis of non-cirrhotic splanchnic vein thrombosis

Magaz, Marta; Alvarez‐Larrán, Alberto; Colomer, Dolors; López‐Guerra, Mònica; García-Criado, Ángeles; Mezzano, Gabriel; Belmonte, Ernest; Olivas, Pol; Soy, Guillem; Cervantes, Francisco; Darnell, Anna; Ferrusquía‐Acosta, José; Baiges, Anna; Turón, Fanny; Hernández‐Gea, Virginia; García‐Pagán, Juan Carlos

doi:10.1016/j.jhep.2020.06.045

Cited by 35 publications

(16 citation statements)

References 49 publications

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“…Even though Carrà’s data mirror those recently published by Magaz et al in 74 patients with idiopathic SVT, 2 the reported results have different points of interest. The first is that the authors, after setting the variant allele frequency threshold as >2%, reported a CHIP prevalence of 46% (95% confidence interval: 21%-73%), which is the highest ever reported.…”

supporting

confidence: 70%

Idiopathic splanchnic vein thrombosis: is it really idiopathic?

Barosi

2022

haematol

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supporting

confidence: 70%

Idiopathic splanchnic vein thrombosis: is it really idiopathic?

Barosi

2022

haematol

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“…The development of computers has made it possible to analyze high-throughput data generated with this approach [ 24 ]. The application of bioinformatics has enriched the diversity of disease research and analysis methods [ 25 ].…”

Section: Discussionmentioning

confidence: 99%

Bioinformatic analysis and preliminary validation of potential therapeutic targets for COVID-19 infection in asthma patients

Liu

Duo

et al. 2022

Cell Commun Signal

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Background Severe acute respiratory syndrome coronavirus 2 causes coronavirus disease 19 (COVID-19). The number of confirmed cases of COVID-19 is also rapidly increasing worldwide, posing a significant challenge to human safety. Asthma is a risk factor for COVID-19, but the underlying molecular mechanisms of the asthma–COVID-19 interaction remain unclear. Methods We used transcriptome analysis to discover molecular biomarkers common to asthma and COVID-19. Gene Expression Omnibus database RNA-seq datasets (GSE195599 and GSE196822) were used to identify differentially expressed genes (DEGs) in asthma and COVID-19 patients. After intersecting the differentially expressed mRNAs, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to identify the common pathogenic molecular mechanism. Bioinformatic methods were used to construct protein–protein interaction (PPI) networks and identify key genes from the networks. An online database was used to predict interactions between transcription factors and key genes. The differentially expressed long noncoding RNAs (lncRNAs) in the GSE195599 and GSE196822 datasets were intersected to construct a competing endogenous RNA (ceRNA) regulatory network. Interaction networks were constructed for key genes with RNA-binding proteins (RBPs) and oxidative stress-related proteins. The diagnostic efficacy of key genes in COVID-19 was verified with the GSE171110 dataset. The differential expression of key genes in asthma was verified with the GSE69683 dataset. An asthma cell model was established with interleukins (IL-4, IL-13 and IL-17A) and transfected with siRNA-CXCR1. The role of CXCR1 in asthma development was preliminarily confirmed. Results By intersecting the differentially expressed genes for COVID-19 and asthma, 393 common DEGs were obtained. GO and KEGG enrichment analyses of the DEGs showed that they mainly affected inflammation-, cytokine- and immune-related functions and inflammation-related signaling pathways. By analyzing the PPI network, we obtained 10 key genes: TLR4, TLR2, MMP9, EGF, HCK, FCGR2A, SELP, NFKBIA, CXCR1, and SELL. By intersecting the differentially expressed lncRNAs for COVID-19 and asthma, 13 common differentially expressed lncRNAs were obtained. LncRNAs that regulated microRNAs (miRNAs) were mainly concentrated in intercellular signal transduction, apoptosis, immunity and other related functional pathways. The ceRNA network suggested that there were a variety of regulatory miRNAs and lncRNAs upstream of the key genes. The key genes could also bind a variety of RBPs and oxidative stress-related genes. The key genes also had good diagnostic value in the verification set. In the validation set, the expression of key genes was statistically significant in both the COVID-19 group and the asthma group compared with the healthy control group. CXCR1 expression was upregulated in asthma cell models, and interference with CXCR1 expression significantly reduced cell viability. Conclusions Key genes may become diagnostic and predictive biomarkers of outcomes in COVID-19 and asthma.

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“…Investigation of the allelic burden with more sensitive techniques such as digital PCR provides more information in this regard. Moreover, investigation of additional somatic variants in JAK2 , in other myeloproliferative associated genes such as MPL or in genes involved in the age and clonal hematopoiesis that have been associated with an increased risk of cardiovascular disease, particularly in DNMT3A, TET2, and ASXL1, could have provided more valuable data [ 45 ].…”

Section: Discussionmentioning

confidence: 99%

Portal Thrombosis in Cirrhosis: Role of Thrombophilic Disorders

Fortea

Carrera

Puente

et al. 2020

JCM

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In patients with liver cirrhosis the contribution of inherited and acquired prothrombotic disorders in the development of non-malignant portal vein thrombosis (PVT) is inconclusive. The purpose of this retrospective study was to examine the prevalence of thrombophilia in this setting at our center from January 2012 to November 2019. Tests included gene mutational analysis for Factor V Leiden, prothrombin G20210A, JAK2 (V617F), Calreticulin (CARL), in addition to activated protein C resistance, antithrombin III, protein C and S levels, and antiphospholipid antibodies. We included 77 patients, six of whom (7.8%) had a thrombophilic disorder: antiphospholipid syndrome in four patients, prothrombin gene mutation in one and factor V Leiden mutation in one. This latter patient had also been diagnosed with polycythemia vera years before PVT development. Complete thrombosis of the main portal vein and re-thrombosis after stopping anticoagulation were more frequent in patients with thrombophilia, but the rates of recanalization under anticoagulant therapy were similar among groups. No other difference was accounted between groups. The low prevalence of acquired and inherited thrombophilia found in patients with cirrhosis and PVT support testing for these disorders on an individual basis and avoiding universal screening to reduce costs and unwarranted testing.

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Next-generation sequencing in the diagnosis of non-cirrhotic splanchnic vein thrombosis

Cited by 35 publications

References 49 publications

Idiopathic splanchnic vein thrombosis: is it really idiopathic?

Idiopathic splanchnic vein thrombosis: is it really idiopathic?

Bioinformatic analysis and preliminary validation of potential therapeutic targets for COVID-19 infection in asthma patients

Portal Thrombosis in Cirrhosis: Role of Thrombophilic Disorders

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