Identification of immune-related genes and susceptible population of pulmonary tuberculosis by constructing TF-miRNA-mRNA regulatory network

Song, Quanquan; Bian, Qin; Liang, Tingting; Zhang, Yinghui; Zhang, Kai

doi:10.1016/j.tube.2021.102139

Cited by 3 publications

(2 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We employed the GeneCards (https://www.genecards.org/) (access date: November 2, 2021) database to explore SOCS3 mRNA expression in normal tissues and found that SOCS3 was highly expressed in the nervous system, reproductive system, immune system, and various visceral tissues (Figure 2A) (30,31). Then, PROTTER (https://wlab.ethz.ch/protter/start/) (access date: November 4, 2021) was used to explore the SOCS3 protein topology.…”

Section: Socs3 Localization Variations and Expression Under Physiolog...mentioning

confidence: 99%

SOCS3 Acts as an Onco-immunological Biomarker With Value in Assessing the Tumor Microenvironment, Pathological Staging, Histological Subtypes, Therapeutic Effect, and Prognoses of Several Types of Cancer

et al. 2022

View full text Add to dashboard Cite

The suppressor of cytokine signaling (SOCS) family contains eight members, including SOCS1–7 and CIS, and SOCS3 has been shown to inhibit cytokine signal transduction in various signaling pathways. Although several studies have currently shown the correlations between SOCS3 and several types of cancer, no pan-cancer analysis is available to date. We used various computational tools to explore the expression and pathogenic roles of SOCS3 in several types of cancer, assessing its potential role in the pathogenesis of cancer, in tumor immune infiltration, tumor progression, immune evasion, therapeutic response, and prognostic. The results showed that SOCS3 was downregulated in most The Cancer Genome Atlas (TCGA) cancer datasets but was highly expressed in brain tumors, breast cancer, esophageal cancer, colorectal cancer, and lymphoma. High SOCS3 expression in glioblastoma multiforme (GBM) and brain lower-grade glioma (LGG) were verified through immunohistochemical experiments. GEPIA and Kaplan–Meier Plotter were used, and this bioinformatics analysis showed that high SOCS3 expression was associated with a poor prognosis in the majority of cancers, including LGG and GBM. Our analysis also indicated that SOCS3 may be involved in tumor immune evasion via immune cell infiltration or T-cell exclusion across different types of cancer. In addition, SOCS3 methylation was negatively correlated with mRNA expression levels, worse prognoses, and dysfunctional T-cell phenotypes in various types of cancer. Next, different analytical methods were used to select genes related to SOCS3 gene alterations and carcinogenic characteristics, such as STAT3, SNAI1, NFKBIA, BCL10, TK1, PGS1, BIRC5, TMC8, and AFMID, and several biological functions were identified between them. We found that SOCS3 was involved in cancer development primarily through the JAK/STAT signaling pathway and cytokine receptor activity. Furthermore, SOCS3 expression levels were associated with immunotherapy or chemotherapy for numerous types of cancer. In conclusion, this study showed that SOCS3 is an immune-oncogenic molecule that may possess value as a biomarker for diagnosis, treatment, and prognosis of several types of cancer in the future.

show abstract

Section: Socs3 Localization Variations and Expression Under Physiolog...mentioning

confidence: 99%

SOCS3 Acts as an Onco-immunological Biomarker With Value in Assessing the Tumor Microenvironment, Pathological Staging, Histological Subtypes, Therapeutic Effect, and Prognoses of Several Types of Cancer

et al. 2022

View full text Add to dashboard Cite

show abstract

“…It has been reported that the expression levels of miR-454-3p, miR-15a-5p, miR-590-5p, miR-381 and miR-449a in patients with pulmonary tuberculosis were signi cantly different from those in healthy controls before treatment 9 . Circulating miRNAs are easy to detect, relatively stable in expression, and have good tissue speci city, making them reliable candidate biomarkers 10 .…”

Section: Introductionmentioning

confidence: 99%

Plasma miR-3192-5p is a Potential biomarker associated with spinal tuberculosis patients

Dai,

Li,

Xiang

et al. 2024

Preprint

View full text Add to dashboard Cite

Background. Spinal tuberculosis (STB) accounts for approximately 50% of all bone and joint tuberculosis cases, and the understanding of the molecular mechanism of spinal tuberculosis remains limited. Accurate biomarkers are needed to diagnose spinal tuberculosis, which will help manage the incidence of spinal tuberculosis. The gold standard for the diagnosis of spinal tuberculosis requires biopsies of the lesions, which often cause the lesions to spread or delay the timing of anti-tuberculosis therapy. Therefore, there is a pressing need to develop noninvasive diagnostic tools. As a candidate diagnostic marker of spinal tuberculosis, circulating microRNAs (miRNAs) have the characteristics of easy detection, good stability, and strong tissue specificity. Methods. The gene expression database was utilized to compare the expression of miRNAs between patients diagnosed with spinal tuberculosis and undiagnosed patients, and the interaction between miRNAs and target genes was analysed to explain their expression and function. A protein‒protein interaction (PPI) network was further constructed. In bioinformatics analysis, RT‒qPCR was used to verify the expression of miRNAs in the BMSC cell line. A receiver operating characteristic (ROC) curve was constructed by using plasma miRNAs from 12 patients with spinal tuberculosis and 12 healthy controls, and its clinical diagnostic value was evaluated. Results. We identified six novel miRNAs as potential candidate diagnostic biomarkers for patients with spinal tuberculosis. In addition, the predicted target genes provide insight into the molecular mechanisms underlying spinal tuberculosis. Conclusion. There was a stable and significant difference in the expression of miR-3192-5p between STB and healthy controls. Our findings may provide reliable candidate biomarkers for the precise diagnosis and individualized treatment of STB and the development of further clinical applications in STB.

show abstract

Comprehensive identification of immuno-related transcriptional signature for active pulmonary tuberculosis by integrated analysis of array and single cell RNA-seq

Tan²,

Zhang³

et al. 2022

Journal of Infection

View full text Add to dashboard Cite

Identification of immune-related genes and susceptible population of pulmonary tuberculosis by constructing TF-miRNA-mRNA regulatory network

Cited by 3 publications

References 45 publications

SOCS3 Acts as an Onco-immunological Biomarker With Value in Assessing the Tumor Microenvironment, Pathological Staging, Histological Subtypes, Therapeutic Effect, and Prognoses of Several Types of Cancer

SOCS3 Acts as an Onco-immunological Biomarker With Value in Assessing the Tumor Microenvironment, Pathological Staging, Histological Subtypes, Therapeutic Effect, and Prognoses of Several Types of Cancer

Plasma miR-3192-5p is a Potential biomarker associated with spinal tuberculosis patients

Comprehensive identification of immuno-related transcriptional signature for active pulmonary tuberculosis by integrated analysis of array and single cell RNA-seq

Contact Info

Product

Resources

About