Biomarkers: Promising and valuable tools towards diagnosis, prognosis and treatment of Covid-19 and other diseases

Bodaghi, Ali; Fattahi, Nadia; Ramazani, Ali

doi:10.1016/j.heliyon.2023.e13323

Cited by 74 publications

(50 citation statements)

References 183 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…19,20 The identification of unique biomarkers through various classification models and feature selection techniques increases the potential for personalized medicine approaches in the treatment of these diseases. 21 The validation of selected genes via qRT-PCR and the high adjusted R 2 values observed across all genes demonstrate the robustness and dependability of the observed gene expression patterns. 22 Validated by both RNA-Seq and qRT-PCR, the significant upregulation of proinflammatory cytokines and molecules implicated in matrix remodelling and angiogenesis emphasizes their central role in the disease process.…”

Section: Discussionmentioning

confidence: 81%

Comparative study on gene expression in psoriatic lesions versus chronic wound healing processes

Qiong,

Dongxue,

Qing

et al. 2023

International Wound Journal

View full text Add to dashboard Cite

Psoriasis and chronic ulcers not only significantly impair quality of life but also pose a challenge in dermatological treatment. This study aimed to identify new therapeutic targets and biomarkers for psoriasis and chronic ulcers by comparing their gene expression profiles. The gene expression profiles of psoriatic, wound and chronic ulcer patients, as well as healthy controls, were determined via RNA extraction and next‐generation sequencing of biopsies. In order to identify biomarkers, functional enrichment, differential expression analysis and machine learning algorithms were implemented. It is worth mentioning that the genes IL17A, TNF, KRT16, MMP9, and CD44 exhibited substantial correlations with the pathogenesis of the conditions being studied. As evidenced by their AUC‐ROC values approaching 0.90, machine learning models accurately identified these biomarkers. The differential gene expression was consequently validated via qRT‐PCR, which highlighted the increased expression of matrix remodelling enzymes and inflammatory cytokines. Additionally, genes essential for maintaining epidermis integrity and facilitating wound healing exhibited downregulation. These insights into the molecular mechanisms of psoriasis and chronic ulcers pave the way for the development of targeted therapies, offering hope for improved treatment strategies.

show abstract

Section: Discussionmentioning

confidence: 81%

Comparative study on gene expression in psoriatic lesions versus chronic wound healing processes

Qiong,

Dongxue,

Qing

et al. 2023

International Wound Journal

View full text Add to dashboard Cite

show abstract

“…In Table 10 , we list some pathogenic species where E. coli PEIs are predicted to co-occur. Hence, experimental investigation of E. coli PEIs may help us to develop novel therapeutic strategies [76] to cure diseases caused by these pathogens.…”

Section: Discussionmentioning

confidence: 99%

The protein interactome ofEscherichia colicarbohydrate metabolism

Chowdhury,

Fong,

Uetz

2024

Preprint

View full text Add to dashboard Cite

Carbohydrate metabolism is strictly regulated by multiple mechanisms to meet cellular needs (i.e. energy production). Several mechanisms modulate the amount and activity of metabolic enzymes. Here, we investigate how carbohydrate metabolism (CHM) inE. coliis regulated by their interaction properties with other proteins and their quantities. We computationally analyze 378 protein-enzyme interactions (PEIs) potentially involved in carbohydrate metabolism. We identified 20 enzymes and 19 interactors that occur at stoichiometries that are highly likely to affect CHM and 174 interactions that are possibly conserved across thousands of bacteria. These PPIs are predicted to be of global importance, including pathogens.Author summaryIn systems biology, “big” data are used to reconstruct biological networks which are then investigated in detail to uncover their functional dynamics. Understanding functional dynamics finally helps in identifying biomarkers in the big networks. We apply this concept to the biological network which is a crosstalk of protein-protein interaction network and carbohydrate metabolic pathway inEscherichia coliK-12. We investigate if proteins regulate enzymes when they bind them and we predict that protein-enzyme interactions (PEIs) regulate carbohydrate metabolism inE. coli.

show abstract

“…Moreover, the biomarker measurements used in these studies are typically collected after the diagnosis of obesity. This raises concerns about potential reverse causation, where the disease itself may influence the biomarker levels, making it challenging to confirm causal underlying mechanisms 22 . To address this limitation and gain more insights, incorporating genetic information can be beneficial.…”

Section: Clinical Biomarkers For Identifying Obesity Subtypesmentioning

confidence: 99%

Identifying obesity subtypes: A review of studies utilising clinical biomarkers and genetic data

Abraham,

Yaghootkar

2023

Diabet Med

View full text Add to dashboard Cite

Obesity is a complex and multifactorial condition that poses significant health risks. Recent advancements in our understanding of obesity have highlighted the heterogeneity within this disorder. Identifying distinct subtypes of obesity is crucial for personalised treatment and intervention strategies. This review paper aims to examine studies that have utilised clinical biomarkers and genetic data to identify clusters or subtypes of obesity. The findings of these studies may provide valuable insights into the underlying mechanisms and potential targeted approaches for managing obesity‐related health issues such as type 2 diabetes.

show abstract

Biomarkers: Promising and valuable tools towards diagnosis, prognosis and treatment of Covid-19 and other diseases

Cited by 74 publications

References 183 publications

Comparative study on gene expression in psoriatic lesions versus chronic wound healing processes

Comparative study on gene expression in psoriatic lesions versus chronic wound healing processes

The protein interactome ofEscherichia colicarbohydrate metabolism

Identifying obesity subtypes: A review of studies utilising clinical biomarkers and genetic data

Contact Info

Product

Resources

About