The Role of Genomics and Proteomics in Lung Cancer Early Detection and Treatment

Abbasian, Mohammad Hadi; Ardekani, Ali M.; Sobhani, Navid; Roudi, Raheleh

doi:10.3390/cancers14205144

Cited by 19 publications

(14 citation statements)

References 181 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To our knowledge, this is the first comprehensive computational analysis using multiple databases that identified GPC3 as a tumor suppressor gene in LUAD and could be used as a novel therapeutic target for the treatment of LUAD. Our study introduces novel insights into the role of GPC3 in LUAD, a topic not addressed in the broader review of NSCLC biomarkers by Abbasian et al [ 31 ] The distinct co-expression profile, mutational aspects, and epigenetic considerations surrounding GPC3 highlight its potential as a critical biomarker in LUAD. This underscores the need for continued exploration of single genes that may hold promise even in well-studied areas such as NSCLC.…”

Section: Discussionmentioning

confidence: 90%

“…In addition, while numerous studies, including a comprehensive review by Abbasian et al, [ 31 ] have highlighted genomic and proteomic biomarkers for the early detection and treatment of NSCLC, the role and importance of GPC3 in LUAD remain underexplored. Therefore, in the current study, we sought to analyze publicly available cancer microarray datasets to investigate the mRNA expression, methylation pattern, and mutational profile (including copy number alterations; CNAs) of GPC3 in LUAD, as well as the relationship among these variables.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Biological and clinical significance of the glypican-3 gene in human lung adenocarcinoma: An in silico analysis

Imon,

Aktar,

Morshed

et al. 2023

Medicine

View full text Add to dashboard Cite

Glypican-3 (GPC3), a membrane-bound heparan sulfate proteoglycan, has long been found to be dysregulated in human lung adenocarcinomas (LUADs). Nevertheless, the function, mutational profile, epigenetic regulation, co-expression profile, and clinicopathological significance of the GPC3 gene in LUAD progression are not well understood. In this study, we analyzed cancer microarray datasets from publicly available databases using bioinformatics tools to elucidate the above parameters. We observed significant downregulation of GPC3 in LUAD tissues compared to their normal counterparts, and this downregulation was associated with shorter overall survival (OS) and relapse-free survival (RFS). Nevertheless, no significant differences in the methylation pattern of GPC3 were observed between LUAD and normal tissues, although lower promoter methylation was observed in male patients. GPC3 expression was also found to correlate significantly with infiltration of B cells, CD8+, CD4+, macrophages, neutrophils, and dendritic cells in LUAD. In addition, a total of 11 missense mutations were identified in LUAD patients, and ~1.4% to 2.2% of LUAD patients had copy number amplifications in GPC3. Seventeen genes, mainly involved in dopamine receptor-mediated signaling pathways, were frequently co-expressed with GPC3. We also found 11 TFs and 7 miRNAs interacting with GPC3 and contributing to disease progression. Finally, we identified 3 potential inhibitors of GPC3 in human LUAD, namely heparitin, gemcitabine and arbutin. In conclusion, GPC3 may play an important role in the development of LUAD and could serve as a promising biomarker in LUAD.

show abstract

Section: Discussionmentioning

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Biological and clinical significance of the glypican-3 gene in human lung adenocarcinoma: An in silico analysis

Imon,

Aktar,

Morshed

et al. 2023

Medicine

View full text Add to dashboard Cite

show abstract

“…In addition, genomics, transcriptomics, proteomics, lipidomics and metabolomics are important to be used to determine the mechanisms of disease development and carcinogenesis [ (Zhou et al, 2019;Zhang et al, 2020b;Boys et al, 2022)]. The role of multi-omics has been described in lung cancer early detection and therapy [ (Abbasian et al, 2022), (Ling et al, 2022)]. The multi-omics should be applied for exploration of TME and immunotherapy in lung cancer to overcome the immunotherapy resistance.…”

Section: Discussionmentioning

confidence: 99%

Nanoparticles overcome adaptive immune resistance and enhance immunotherapy via targeting tumor microenvironment in lung cancer

et al. 2023

View full text Add to dashboard Cite

Lung cancer is one of the common malignant cancers worldwide. Immune checkpoint inhibitor (ICI) therapy has improved survival of lung cancer patients. However, ICI therapy leads to adaptive immune resistance and displays resistance to PD-1/PD-L1 blockade in lung cancer, leading to less immune response of lung cancer patients. Tumor microenvironment (TME) is an integral tumor microenvironment, which is involved in immunotherapy resistance. Nanomedicine has been used to enhance the immunotherapy in lung cancer. In this review article, we described the association between TME and immunotherapy in lung cancer. We also highlighted the importance of TME in immunotherapy in lung cancer. Moreover, we discussed how nanoparticles are involved in regulation of TME to improve the efficacy of immunotherapy, including Nanomedicine SGT-53, AZD1080, Nanomodulator NRF2, Cisplatin nanoparticles, Au@PG, DPAICP@ME, SPIO NP@M-P, NBTXR3 nanoparticles, ARAC nanoparticles, Nano-DOX, MS NPs, Nab-paclitaxel, GNPs-hPD-L1 siRNA. Furthermore, we concluded that targeting TME by nanoparticles could be helpful to overcome resistance to PD-1/PD-L1 blockade in lung cancer.

show abstract

“…Understanding the functional roles of proteins and proteomes can help to understand several diseases and abnormalities at the cellular level. − In particular, studying changes in the expression level, turnover, subcellular localization, regulation, protein–protein interactions (PPI), networking, cell signaling cascades, and post-translational modifications may lead to important insights regarding key cellular mechanisms.…”

Section: Introductionmentioning

confidence: 99%

Cytoplasmic Shotgun Proteomic Points to Key Proteins and Pathways in Temozolomide-Resistant Glioblastoma Multiforme

Teraiya,

Krokhin,

Chen

et al. 2023

J. Proteome Res.

View full text Add to dashboard Cite

Temozolomide (TMZ) is the first line of chemotherapy to treat primary brain tumors of the type glioblastoma multiforme (GBM). TMZ resistance (TMZR) is one of the main barriers to successful treatment and is a principal factor in relapse, resulting in a poor median survival of 15 months. The present paper focuses on proteomic analyses of cytosolic fractions from TMZ-resistant (TMZR) LN-18 cells. The experimental workflow includes an easy, cost-effective, and reproducible method to isolate subcellular fraction of cytosolic (CYTO) proteins, mitochondria, and plasma membrane proteins for proteomic studies. For this study, enriched cytoplasmic fractions were analyzed in replicates by nanoflow liquid chromatography tandem high-resolution mass spectrometry (nLC-MS/MS), and proteins identified were quantified using a label-free approach (LFQ). Statistical analysis of control (CTRL) and temozolomide-resistant (TMZR) proteomes revealed proteins that appear to be differentially controlled in the cytoplasm. The functions of these proteins are discussed as well as their roles in other cancers and TMZ resistance in GBM. Key proteins are also described through biological processes related to gene ontology (GO), molecular functions, and cellular components. For protein–protein interactions (PPI), network and pathway involvement analyses have been performed, highlighting the roles of key proteins in the TMZ resistance phenotypes. This study provides a detailed insight into methods of subcellular fractionation for proteomic analysis of TMZ-resistant GBM cells and the potential to apply this approach to future large-scale studies. Several key proteins, protein–protein interactions (PPI), and pathways have been identified, underlying the TMZ resistance phenotype and highlighting the proteins’ biological functions.

show abstract

The Role of Genomics and Proteomics in Lung Cancer Early Detection and Treatment

Cited by 19 publications

References 181 publications

Biological and clinical significance of the glypican-3 gene in human lung adenocarcinoma: An in silico analysis

Biological and clinical significance of the glypican-3 gene in human lung adenocarcinoma: An in silico analysis

Nanoparticles overcome adaptive immune resistance and enhance immunotherapy via targeting tumor microenvironment in lung cancer

Cytoplasmic Shotgun Proteomic Points to Key Proteins and Pathways in Temozolomide-Resistant Glioblastoma Multiforme

Contact Info

Product

Resources

About