Mathematical analysis of gefitinib resistance of lung adenocarcinoma caused by MET amplification

Comprehensive analyses of genome-wide methylation and RNA epigenetics identify prognostic biomarkers, regulating the tumor immune microenvironment in lung adenocarcinoma

The aim of our study was to identify a signature of immune-regulated molecules and reveal its prognostic role in lung adenocarcinoma (LUAD). We downloaded RNA-Sequencing data and DNA methylation data from the Gene Expression Omnibus (GEO) database. GEO2R was used to analyze differentially expressed mRNAs (DEmRNAs). we used "factoextra" R package to do the principal component analysis (PCA) of DEmRNAs. "Limma" R package was used to identify DEmRNAs, differentially expressed miRNAs (DEmiRNAs), differentially expressed lncRNAs (DElncRNAs) from The Cancer Genome Atlas (TCGA) database. Three R packages "org.Hs.eg.db", "clusterProfiler", "ggplot2″ were used to show enrichment results. Considering about methylation and mutation data, TEK and SOX17 mediated cancer signaling pathways. Through tumor-immune system interactions database (TISIDB) and Tumor Immune Estimation Resource (TIMER), higher methylated and lower expressed TEK may act as a prognostic marker, regulating the tumor immunity in LUAD. Through four databases (MEXPRESS, DNMIVD, MethSurv, Firehose), we further verified the methylation (P = 2.33e-23) and mutation about TEK. A signature of immune-associated TEK to predict survival of LUAD patients was validated. Prognostic, methylation, immune microenvironment analysis showed new light on potential novel therapeutic targets in LUAD.

CHEK1: a hub gene related to poor prognosis for lung adenocarcinoma

Aim: The study aims to pinpoint hub genes and investigate their functions in order to gain insightful understandings of lung adenocarcinoma (LUAD). Methods: Bioinformatic approaches were adopted to investigate genes in databases including Gene Expression Omnibus, WebGestalt, STRING and Cytoscape, GEPIA2, Oncomine, Human Protein Atlas, TIMER2.0, UALCAN, cBioPortal, TargetScanHuman, OncomiR, ENCORI, Kaplan-Meier plotter, UCSC Xena, European Molecular Biology Laboratory - European Bioinformatics Institute Single Cell Expression Atlas and CancerSEA. Results: Five hub genes were ascertained. CHEK1 was overexpressed in a range of cancers, including LUAD. Promoter methylation, amplification and miRNA regulation might trigger CHEK1 upregulation, signaling poor prognosis. CHEK1 with its coexpressed genes were enriched in the cell cycle pathway. Intratumor heterogeneity of CHEK1 expression could be observed. Cell clusters with CHEK1 expression were more prone to metastasis and epithelial-to-mesenchymal transition. Conclusion: CHEK1 might potentially act as a prognostic biomarker for LUAD.

Macrophage membrane-mediated targeted drug delivery for treatment of spinal cord injury regardless of the macrophage polarization states

Targeted delivery of therapeutics for spinal cord injury (SCI) has been a long-term challenge due to the complexity of the pathological procession. Macrophage, as an immune cell, can selectively accumulate at the trauma site after SCI. This intrinsic targeting, coupled with good immune-escaping capacity makes macrophages an ideal source of biomimetic delivery carrier for SCI. Worth mentioning, macrophages have multiple polarization states, which may not be ignored when designing macrophage-based delivery systems. Herein, we fabricated macrophage membrane-camouflaged liposomes (RM-LIPs) and evaluated their abilities to extend drug circulation time and target the injured spinal cord. Specially, we detected the expression levels of the two main targeted receptors Mac-1 and integrin α4 in three macrophage subtypes, including unactivated (M0) macrophages, classically activated (M1) macrophages and alternatively activated (M2) macrophages, and compared targeting of these macrophage membrane-coated nanoparticles for SCI. The macrophage membrane camouflage decreased cellular uptake of liposomes in RAW264.7 immune cells and strengthened binding of the nanoparticle to the damaged endothelial cells in vitro. RM-LIPs can prolong drug circulation time and actively accumulate at the trauma site of the spinal cord in vivo. Besides, RM-LIPs loaded with minocycline (RM-LIP/MC) showed a comprehensive therapeutic effect on SCI mice, and the anti-pyroptosis was found to be a novel mechanism of RM-LIP/MC treatment of SCI. Moreover, the levels of Mac-1 and integrin α4 in macrophages and the targeting of RM-LIP for SCI were found to be independent of macrophage polarization states. Our study provided a biomimetic strategy via the biological properties of macrophages for SCI targeting and treatment.

NFAT indicates nucleocytoplasmic damped oscillation via its feedback modulator

Cell signaling and the following gene regulation are tightly regulated to keep homeostasis. NF-κB is a famous key transcription factor for inflammatory cell regulations that obtain a closed feedback loop with IκB. Similarly, we show here, NFAT is also tightly regulated via its downstream target, down syndrome critical region (DSCR)-1. In primary cultured endothelium, either shear stress or VEGF treatment revealed quick NFAT1 nuclear localization following the DSCR-1 transactivation, which in turn induced NFAT1 cytoplasm sequestration. Interestingly, both NFAT and DSCR-1 can be competitive substrates for calcineurin phosphatase and DSCR-1 is known to unstable protein, which caused NFAT1-nucleocytoplasmic damped oscillation via sustained shear stress or VEGF stimulation in endothelial cell (EC)s. To understand the molecular mechanism underlying the NFAT1 oscillation, we built a mathematical model of spatiotemporal regulation of NFAT1 combined with calcineurin and DSCR-1. Theoretically, manipulation of DSCR-1 expression in simulation predicted that DSCR-1 reduction would cause nuclear retention of dephosphorylated NFAT1 and disappearance of NFAT1 oscillation. To confirm this in ECs, DSCR-1 knockdown analysis was performed. DSCR-1 reduction indeed increased dephosphorylated NFAT1 in both the nucleus and cytoplasm, which eventually led to nuclear retention of NFAT1. Taken together, these studies suggest that DSCR-1 is a responsible critical factor for NFAT1 nucleocytoplasmic oscillation in shear stress or VEGF treated ECs. Our mathematical model successfully reproduced the experimental observations of NFAT1 dynamics. Combined mathematical and experimental approaches would provide a quantitative understanding way for the spatiotemporal NFAT1 feedback system.

Identification of prognostic markers of lung cancer through bioinformatics analysis and in vitro experiments

Lung cancer is one of the most common types of cancer worldwide. Understanding the molecular mechanisms underlying the development and progression of lung cancer may improve early diagnosis, treatment and prognosis. The aim of the present study was to examine the pathogenesis of lung cancer and to identify potentially novel biomarkers. Gene expression datasets of patients with lung cancer were obtained from the Gene Expression Omnibus. Genes which were most closely associated with lung cancer (core genes) were screened by weighted gene co‑expression network analysis. In vitro cell based experiments were further utilized to verify the effects of the core genes on the proliferation of lung cancer cells, adhesion between cells and the matrix, and the associated metabolic pathways. Based on WGCNA screening, two gene modules and five core genes closely associated with lung cancer, including immunoglobulin superfamily member 10 (IGSF10) from the turquoise module, and ribonucleotide reductase regulatory subunit M2, protein regulator of cytokinesis 1, kinesin family member (KIF)14 and KIF2C from the brown module were identified as relevant. Survival analysis and differential gene expression analysis showed that there were significant differences in IGSF10 expression levels between the healthy controls and patients with lung cancer. In patients with lung cancer, IGSF10 expression was decreased, and the overall survival time of patients with lung cancer was significantly shortened. An MTT and colony formation assay showed that IGSF10‑knockout significantly increased proliferation of lung cancer cells, and Transwell assays and adhesion experiments further suggested that the adhesion between cells and the matrix was significantly increased in IGSF10‑knockout cells. Gene Set Enrichment Analysis showed that the expression level of IGSF10 was significantly associated with the activation of the integrin‑β1/focal adhesion kinase (FAK) pathway. Western blotting revealed that knockout of IGSF10 resulted in the activation of the integrin‑β1/FAK pathway, as the protein expression levels of integrin‑β1, phosphorylated (p)‑FAK and p‑AKT were significantly upregulated. Activation of the integrin‑β1/FAK pathway, following knockout of IGSF10, affected the proliferation and adhesion of lung cancer cells. Therefore, IGSF10 my serve as a potential prognostic marker of lung cancer.

Cooperativity transitions driven by higher-order oligomer formations in ligand-induced receptor dimerization

While cooperativity in ligand-induced receptor dimerization has been linked with receptor-receptor couplings via minimal representations of physical observables, effects arising from higher-order oligomer, e.g., trimer and tetramer, formations of unobserved receptors have received less attention. Here we propose a dimerization model of ligand-induced receptors in multivalent form representing physical observables under basis vectors of various aggregated receptor states. Our simulations of multivalent models not only reject Wofsy-Goldstein parameter conditions for cooperativity, but show that higher-order oligomer formations can shift cooperativity from positive to negative.

FGFR1 Induces Acquired Resistance Against Gefitinib By Activating AKT/mTOR Pathway In NSCLC

Objective

As an epidermal growth factor, receptor-tyrosine kinase inhibitor (EGFR-TKI), gefitinib demonstrates a good therapeutic effect in patients with EGFR-mutant non-small-cell lung cancer (NSCLC). However, an overwhelming majority of these patients inevitably develop resistance against gefitinib. Unfortunately, the mechanism underlying this phenomenon is still not fully understood. Here we aim to reveal the mechanism of gefitinib resistance in NSCLC induced by FGFR1.

Materials and methods

We used high-throughput sequencing to compare the mRNA expression profiles of PC9 and PC9-GR (gefitinib-resistant) cells. The clinical significance of fibroblast growth factor receptor 1 (FGFR1) in NSCLC was also investigated using immunohistochemistry and Kaplan-Meier survival analysis. Finally, the in vitro molecular mechanisms were analyzed using confocal laser microscopy, Western blotting, transwell assay, colony formation assay, CCK-8 assay, and apoptosis assay.

Results

We observed that FGFR1 was highly expressed in NSCLC tissues and was closely associated with poor prognosis. Cytological experiments showed that FGFR1 promoted the proliferation and migration of PC9-GR cells and mediated their resistance to gefitinib. Furthermore, studies aimed at unraveling this mechanism revealed that FGFR1 activated the AKT/mTOR signaling pathway. These findings show that the FGFR1/AKT/mTOR signaling pathway plays a vital role in acquired resistance against gefitinib in NSCLC.

Conclusion

This work provides new evidence that FGFR1 functions as a key regulator of gefitinib resistance, thereby demonstrating its potential as a novel biomarker and therapeutic target for NSCLC.

Drug resistance to targeted therapeutic strategies in non-small cell lung cancer

Rapidly developing molecular biology techniques have been employed to identify cancer driver genes in specimens from patients with non-small cell lung cancer (NSCLC). Inhibitors and antibodies that specifically target driver gene-mediated signaling pathways to suppress tumor growth and progression are expected to extend the survival time and further improve the quality of life of patients. However, the health of patients with advanced and metastatic NSCLC presents significant challenges due to treatment resistance, mediated by cancer driver gene alteration, epigenetic alteration, and tumor heterogeneity. In this review, we discuss two different resistance mechanisms in NSCLC targeted therapies, namely changes in the targeted oncogenes (on-target resistance) and changes in other related signaling pathways (off-target resistance) in tumor cells. We highlight the conventional mechanisms of drug resistance elicited by the complex heterogeneous microenvironment of NSCLC during targeted therapy, including mutations in epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), the receptor tyrosine kinase ROS proto-oncogene 1 (ROS1), and the serine/threonine-protein kinase BRAF (v-Raf murine sarcoma viral oncogene homolog B). We also discuss the mechanism of action of less common oncoproteins, as in-depth understanding of these molecular mechanisms is important for optimizing treatment strategies.

The TGFβ-miR-499a-SHKBP1 pathway induces resistance to EGFR inhibitors in osteosarcoma cancer stem cell-like cells

Background/aims

A novel paradigm in tumor biology suggests that osteosarcoma (OS) chemo-resistance is driven by osteosarcoma stem cell-like cells (OSCs). As the sensitivity of only a few tumors to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) can be explained by the presence of EGFR tyrosine kinase (TK) domain mutations, there is a need to elucidate mechanisms of resistance to EGFR-targeted therapies in OS that do not harbor TK sensitizing mutations to develop new strategies to circumvent resistance to EGFR inhibitors.

Methods

As a measure of the characters of OSCs, serum-free cultivation, cell viability test with erlotinib, and serial transplantation in vivo was used. Western blot assays were used to detect the association between erlotinib resistance and transforming growth factor beta (TGFβ)-induced epithelial-to-mesenchymal transition (EMT) progression. By using TaqMan qPCR miRNA array, online prediction software, luciferase reporter assays and western blot analysis, we further elucidated the mechanisms.

Results

Here, CD166⁺ cells are found in 10 out of 10 tumor samples. We characterize that CD166⁺ cells from primary OS tissues bear hallmarks of OSCs and erlotinib-resistance. TGFβ-induced EMT-associated kinase switch is demonstrated to promote erlotinib-resistance of CD166⁺ OSCs. Further mechanisms study show that TGFβ-induced EMT decreases miR-499a expression through the direct binding of Snail1/Zeb1 to miR-499a promoter. Overexpression of miR-499a in CD166⁺ OSCs inhibits TGFβ-induced erlotinib-resistance in vitro and in vivo. SHKBP1, the direct target of miR-499a, regulates EGFR activity reduction occurring concomitantly with a TGFβ-induced EMT-associated kinase switch to an AKT-activated EGFR-independent state. TGFβ-induced activation of AKT co-opts an increased SHKBP1 expression, which further regulates EGFR activity. In clinic, the ratio of the expression levels of SHKBP1 and miR-499a is highly correlated with EMT and resistance to erlotinib.

Conclusion

TGFβ–miR-499a–SHKBP1 network orchestrates the EMT-associated kinase switch that induces resistance to EGFR inhibitors in CD166⁺ OSCs, implies that inhibition of TGFβ induced EMT-associated kinase switch may reverse the chemo-resistance of OSCs to EGFR inhibitors. We also suggest that an elevated SHKBP1/miR-499a ratio is a molecular signature that characterizes the erlotinib-resistant OS, which may have clinical value as a predictive biomarker.

Electronic supplementary material

The online version of this article (10.1186/s13046-019-1195-y) contains supplementary material, which is available to authorized users.