Profiling of subcellular EGFR interactome reveals hnRNP A3 modulates nuclear EGFR localization

Nuclear epidermal growth factor receptor (nEGFR) in clinical treatment

The epidermal growth factor receptor (EGFR) is a recognized target in tumor treatment. While there is significant focus on inhibiting membrane EGFR and its downstream signaling activation, the ectopic accumulation of EGFR, particularly nuclear EGFR (nEGFR), has been implicated in tumor-associated activities and associated with poor prognosis. Within the nucleus, nEGFR functions as a transcriptional regulator to modulate transcriptional landscape and exerts tyrosine kinase activity to phosphorylate nuclear proteins and subsequently influences DNA repair, cell cycle, proliferation, and resistance to radiotherapy and chemotherapy. The nuclear localization of EGFR involves the internalization, subcellular trafficking, and nuclear envelope shuttling of membrane EGFR. Given the challenges of delivering drugs to the nucleus for targeting nEGFR, understanding the molecules affecting the translocation process is crucial for novel insights. This review initially explores the association between nEGFR expression and clinical outcomes and then elucidates how nEGFR fulfills its regulatory role within the nucleus. Subsequently, the mechanisms governing EGFR nuclear translocation and potential therapeutic targets during this process are summarized, highlighting avenues to target nEGFR as an innovative strategy in tumor treatment.

SubCELL: the landscape of subcellular compartment-specific molecular interactions

The subcellular compartment-specific molecular interactions (SCSIs) are the building blocks for most molecular functions, biological processes and disease pathogeneses. Extensive experiments have therefore been conducted to accumulate the valuable information of SCSIs, but none of the available databases has been constructed to describe those data. In this study, a novel knowledge base SubCELL is thus introduced to depict the landscape of SCSIs among DNAs/RNAs/proteins. This database is UNIQUE in (a) providing, for the first time, the experimentally-identified SCSIs, (b) systematically illustrating a large number of SCSIs inferred based on well-established method and (c) collecting experimentally-determined subcellular locations for the DNAs/RNAs/proteins of diverse species. Given the essential physiological/pathological role of SCSIs, the SubCELL is highly expected to have great implications for modern molecular biological study, which can be freely accessed with no login requirement at: https://idrblab.org/subcell/.

Development of nanoparticles incorporated with quercetin and ACE2-membrane as a novel therapy for COVID-19

INTRODUCTION

Angiotensin-converting enzyme 2 (ACE2) and AXL tyrosine kinase receptor are known to be involved in the SARS-CoV-2 entry of the host cell. Therefore, targeting ACE2 and AXL should be an effective strategy to inhibit virus entry into cells. However, developing agents that can simultaneously target ACE2 and AXL remains a formidable task. The natural compound quercetin has been shown to inhibit AXL expression.

MATERIALS AND METHODS

In this study, we employed PLGA nanoparticles to prepare nanoparticles encapsulated with quercetin, coated with ACE2-containing cell membranes, or encapsulated with quercetin and then coated with ACE-2-containing cell membranes. These nanoparticles were tested for their abilities to neutralize or inhibit viral infection.

RESULTS

Our data showed that nanoparticles encapsulated with quercetin and then coated with ACE2-containing cell membrane inhibited the expression of AXL without causing cytotoxic activity. Nanoparticles incorporated with both quercetin and ACE2-containing cell membrane were found to be able to neutralize pseudo virus infection and were more effective than free quercetin and nanoparticles encapsulated with quercetin at inhibition of pseudo virus and SARS-CoV-2 infection.

CONCLUSIONS

We have shown that the biomimetic nanoparticles incorporated with both ACE-2 membrane and quercetin showed the most antiviral activity and may be further explored for clinical application.

Using tumor habitat-derived radiomic analysis during pretreatment 18F-FDG PET for predicting KRAS/NRAS/BRAF mutations in colorectal cancer

BACKGROUND

To investigate the association between Kirsten rat sarcoma viral oncogene homolog (KRAS) / neuroblastoma rat sarcoma viral oncogene homolog (NRAS) /v-raf murine sarcoma viral oncogene homolog B (BRAF) mutations and the tumor habitat-derived radiomic features obtained during pretreatment 18F-fluorodeoxyglucose (FDG) positron emission tomography (PET) in patients with colorectal cancer (CRC).

METHODS

We retrospectively enrolled 62 patients with CRC who had undergone 18F-FDG PET/computed tomography from January 2017 to July 2022 before the initiation of therapy. The patients were randomly split into training and validation cohorts with a ratio of 6:4. The whole tumor region radiomic features, habitat-derived radiomic features, and metabolic parameters were extracted from 18F-FDG PET images. After reducing the feature dimension and selecting meaningful features, we constructed a hierarchical model of KRAS/NRAS/BRAF mutations by using the support vector machine. The convergence of the model was evaluated by using learning curve, and its performance was assessed based on the area under the receiver operating characteristic curve (AUC), calibration curve, and decision curve analysis. The SHapley Additive exPlanation was used to interpret the contributions of various features to predictions of the model.

RESULTS

The model constructed by using habitat-derived radiomic features had adequate predictive power with respect to KRAS/NRAS/BRAF mutations, with an AUC of 0.759 (95% CI: 0.585-0.909) on the training cohort and that of 0.701 (95% CI: 0.468-0.916) on the validation cohort. The model exhibited good convergence, suitable calibration, and clinical application value. The results of the SHapley Additive explanation showed that the peritumoral habitat and a high_metabolism habitat had the greatest impact on predictions of the model. No meaningful whole tumor region radiomic features or metabolic parameters were retained during feature selection.

CONCLUSION

The habitat-derived radiomic features were found to be helpful in stratifying the status of KRAS/NRAS/BRAF in CRC patients. The approach proposed here has significant implications for adjuvant treatment decisions in patients with CRC, and needs to be further validated on a larger prospective cohort.

Identification of Myelin Basic Protein Proximity Interactome Using TurboID Labeling Proteomics

Myelin basic protein (MBP) is one of the key structural elements of the myelin sheath and has autoantigenic properties in multiple sclerosis (MS). Its intracellular interaction network is still partially deconvoluted due to the unfolded structure, abnormally basic charge, and specific cellular localization. Here we used the fusion protein of MBP with TurboID, an engineered biotin ligase that uses ATP to convert biotin to reactive biotin-AMP that covalently attaches to nearby proteins, to determine MBP interactome. Despite evident benefits, the proximity labeling proteomics technique generates high background noise, especially in the case of proteins tending to semi-specific interactions. In order to recognize unique MBP partners, we additionally mapped protein interaction networks for deaminated MBP variant and cyclin-dependent kinase inhibitor 1 (p21), mimicking MBP in terms of natively unfolded state, size and basic amino acid clusters. We found that in the plasma membrane region, MBP is colocalized with adhesion proteins occludin and myelin protein zero-like protein 1, solute carrier family transporters ZIP6 and SNAT1, Eph receptors ligand Ephrin-B1, and structural components of the vesicle transport machinery-synaptosomal-associated protein 23 (SNAP23), vesicle-associated membrane protein 3 (VAMP3), protein transport protein hSec23B and cytoplasmic dynein 1 heavy chain 1. We also detected that MBP potentially interacts with proteins involved in Fe²⁺ and lipid metabolism, namely, ganglioside GM2 activator protein, long-chain-fatty-acid-CoA ligase 4 (ACSL4), NADH-cytochrome b5 reductase 1 (CYB5R1) and metalloreductase STEAP3. Assuming the emerging role of ferroptosis and vesicle cargo docking in the development of autoimmune neurodegeneration, MBP may recruit and regulate the activity of these processes, thus, having a more inclusive role in the integrity of the myelin sheath.

Cell-Based Sensors for the Detection of EGF and EGF-Stimulated Ca2+ Signaling

Epidermal growth factor (EGF)-mediated activation of EGF receptors (EGFRs) has become an important target in drug development due to the implication of EGFR-mediated cellular signaling in cancer development. While various in vitro approaches are developed for monitoring EGF-EGFR interactions, they have several limitations. Herein, we describe a live cell-based sensor system that can be used to monitor the interaction of EGF and EGFR as well as the subsequent signaling events. The design of the EGF-detecting sensor cells is based on the split-intein-mediated conditional protein trans-cleavage reaction (CPC). CPC is triggered by the presence of the target (EGF) to activate a signal peptide that translocates the fluorescent cargo to the target cellular location (mitochondria). The developed sensor cell demonstrated excellent sensitivity with a fast response time. It was also successfully used to detect an agonist and antagonist of EGFR (transforming growth factor-α and Cetuximab, respectively), demonstrating excellent specificity and capability of screening the analytes based on their function. The usage of sensor cells was then expanded from merely detecting the presence of target to monitoring the target-mediated signaling cascade, by exploiting previously developed Ca²⁺-detecting sensor cells. These sensor cells provide a useful platform for monitoring EGF-EGFR interaction, for screening EGFR effectors, and for studying downstream cellular signaling cascades.

Heterogeneous nuclear ribonucleoprotein A/B: an emerging group of cancer biomarkers and therapeutic targets

Heterogeneous nuclear ribonucleoprotein A/B (hnRNPA/B) is one of the core members of the RNA binding protein (RBP) hnRNPs family, including four main subtypes, A0, A1, A2/B1 and A3, which share the similar structure and functions. With the advance in understanding the molecular biology of hnRNPA/B, it has been gradually revealed that hnRNPA/B plays a critical role in almost the entire steps of RNA life cycle and its aberrant expression and mutation have important effects on the occurrence and progression of various cancers. This review focuses on the clinical significance of hnRNPA/B in various cancers and systematically summarizes its biological function and molecular mechanisms.

Ligand-mediated nanomedicines against breast cancer: a review

Ligand-mediated targeting represents the cutting edge in precision-guided therapy for several diseases. Surface engineering of nanomedicines with ligands exhibiting selective or tailored affinity for overexpressed biomolecules of a specific disease may increase therapeutic efficiency and reduce side effects and recurrence. This review focuses on newly developed approaches and strategies to improve treatment and overcome the mechanisms associated with breast cancer resistance.

Dynamic EGFR interactomes reveal differential association of signaling modules with wildtype and Exon19-del EGFR in NSCLC cell lines

Protein-protein interaction networks (PPIs) govern the majority of biological processes, but how oncogenic mutations impact these interactions and their functions at a network scale is poorly understood. Mutations of epidermal growth factor receptor (EGFR) in non-small cell lung cancer (NSCLC) is a pre-requisition for EGFR tyrosine kinase inhibitor (TKI) treatment. Identification of interaction partners that bind to mutated EGFR can help understand the mechanism of action and pathways that mediate drug resistance. In this study, we characterized the dynamic interaction network of a pair of EGFR wildtype and mutant NSCLC cell lines. We performed immunoprecipitation of endogenous EGFR at various time points following EGF treatment and analyzed the associated proteins by quantitative mass spectrometry. Our results showed that the core signaling modules and key downstream pathways are maintained in the mutant cell line, but receptor internalization and intracellular trafficking in the mutant is delayed. Furthermore, we identified mutant EGFR-associated proteins that could affect EGFR functions in lung adenocarcinoma. SIGNIFICANCE: We analyzed the dynamic EGFR interaction network in NSCLC cell lines expressing wild-type and mutant EGFR. By comparing the similarities and differences in the EGFR proteome, we gained a better understanding of EGFR signal transduction network, and identified new factors for further functional characterizations and clinical significance assessment.

RNA-binding protein p54nrb/NONO potentiates nuclear EGFR-mediated tumorigenesis of triple-negative breast cancer

Nuclear-localized epidermal growth factor receptor (EGFR) highly correlates with the malignant progression and may be a promising therapeutic target for breast cancer. However, molecular mechanisms of nuclear EGFR in triple-negative breast cancer (TNBC) have not been fully elucidated. Here, we performed gene-annotation enrichment analysis for the interactors of nuclear EGFR and found that RNA-binding proteins (RBPs) were closely associated with nuclear EGFR. We further demonstrated p54^nrb/NONO, one of the RBPs, significantly interacted with nuclear EGFR. NONO was upregulated in 80 paired TNBC tissues and indicated a poor prognosis. Furthermore, NONO knockout significantly inhibited TNBC proliferation in vitro and in vivo. Mechanistically, NONO increased the stability of nuclear EGFR and recruited CREB binding protein (CBP) and its accompanying E1A binding protein p300, thereby enhancing the transcriptional activity of EGFR. In turn, EGFR positively regulated the affinity of NONO to mRNAs of nuclear EGFR downstream genes. Furthermore, the results indicated that the nuclear EGFR/NONO complex played a critical role in tumorigenesis and chemotherapy resistance. Taken together, our findings indicate that NONO enhances nuclear EGFR-mediated tumorigenesis and may be a potential therapeutic target for TNBC patients with nuclear EGFR expression.

Facilitating GL13K Peptide Grafting on Polyetheretherketone via 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide: Surface Properties and Antibacterial Activity

In the present work, the antimicrobial peptide (AMP) of GL13K was successfully coated onto a polyetheretherketone (PEEK) substrate to investigate its antibacterial activities against Staphylococcus aureus (S. aureus) bacteria. To improve the coating efficiency, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) was mixed with a GL13K solution and coated on the PEEK surface for comparison. Both energy-dispersive X-ray spectroscopy (EDX) and X-ray photoelectron spectroscopy (XPS) data confirmed 30% greater peptide coating on PEEK/GL13K-EDC than PEEK without EDC treatment. The GL13K graft levels are depicted in the micrograms per square centimeter range. The PEEK/GL13K-EDC sample showed a smoother and lower roughness (Rq of 0.530 µm) than the PEEK/GL13K (0.634 µm) and PEEK (0.697 µm) samples. The surface of the PEEK/GL13K-EDC was more hydrophilic (with a water contact angle of 24°) than the PEEK/GL13K (40°) and pure PEEK (89°) samples. The pure PEEK disc did not exhibit any inhibition zone against S. aureus. After peptide coating, the samples demonstrated significant zones of inhibition: 28 mm and 25 mm for the PEEK/GL13K-EDC and PEEK/GL13K samples, respectively. The bacteria-challenged PEEK sample showed numerous bacteria clusters, whereas PEEK/GL13K contained a little bacteria and PEEK/GL13K-EDC had no bacterial attachment. The results confirm that the GL13K peptide coating was able to induce antibacterial and biofilm-inhibitory effects. To the best of our knowledge, this is the first report of successful GL13K peptide grafting on a PEEK substrate via EDC coupling. The present work illustrates a facile and promising coating technique for a polymeric surface to provide bactericidal activity and biofilm resistance to medical implantable devices.

Effect of EGFR on SQSTM1 Expression in Malignancy and Tumor Progression of Oral Squamous Cell Carcinoma

Oral squamous cell carcinoma (OSCC) is one of the most common types of malignant tumor. Sequestosome 1 (SQSTM1) serves as an adaptor of autophagy for degrading protein aggregates. The regulation of autophagy by EGFR and its clinical impacts are indicated in various types of cancer. However, the association of EGFR and SQSTM1 in OSCC is still unknown. Our results show that the expression levels of SQSTM1 and EGFR proteins are higher in tumor tissues than in the corresponding tumor-adjacent (CTAN) tissues of OSCC patients. The expression levels of SQSTM1 were positively associated with the EGFR expression level. High co-expression of SQSTM1 and EGFR is associated with poor prognosis in OSCC patients. Moreover, SQSTM1 expression is decreased in EGFR-knockdown cells. Cell growth and invasion/migration are also decreased in cells with single/combined knockdowns of EGFR and SQSTM1 or in SQSTM1-knockdown cells without EGFR kinase inhibitor Lapatinib treatment compared to that in scrambled cells. However, cell growth and invasion/metastasis were not significantly different between the scrambled cells and SQSTM1-knockdown cells in the presence of Lapatinib. This study is the first to indicate the biological roles and clinical significance of SQSTM1 regulation by EGFR in OSCC.

A glimpse on the architecture of hnRNP C1/C2 interaction network in cultured oligodendrocytes

hnRNP represent a large family of RNA-binding proteins related to regulation of transcriptional and translational processes. More specifically, hnRNPs play pivotal roles in the myelination of the central nervous system. The regulation of these proteins are associated with neurodegenerative and psychiatric disorders, including schizophrenia. hnRNPs were shown differentially regulated on schizophrenia postmortem brain tissue as well as in cultured oligodendrocytes treated with clozapine, a common antipsychotic used in schizophrenia treatment. Here we employed co-immunoprecipitation of hnRNP C1/C2 to investigate for the first time in a large-scale manner its interaction partners on cultured oligodendrocytes (MO3.13). Even preliminarily, results bring a more comprehensive description of hnRNP C1/C2 interaction network, and therefore insights regarding the potential role of this protein in the central nervous system in health and disease, warranting further investigation.

hnRNP A/B Proteins: An Encyclopedic Assessment of Their Roles in Homeostasis and Disease

The hnRNP A/B family of proteins is canonically central to cellular RNA metabolism, but due to their highly conserved nature, the functional differences between hnRNP A1, A2/B1, A0, and A3 are often overlooked. In this review, we explore and identify the shared and disparate homeostatic and disease-related functions of the hnRNP A/B family proteins, highlighting areas where the proteins have not been clearly differentiated. Herein, we provide a comprehensive assembly of the literature on these proteins. We find that there are critical gaps in our grasp of A/B proteins' alternative splice isoforms, structures, regulation, and tissue and cell-type-specific functions, and propose that future mechanistic research integrating multiple A/B proteins will significantly improve our understanding of how this essential protein family contributes to cell homeostasis and disease.

Regulation of EGFR activation and signaling by lipids on the plasma membrane

Lipids on the plasma membrane are not only components of the membrane biophysical structures but also regulators of receptor functions. Recently, the critical roles of lipid-protein interactions have been intensively highlighted. Epidermal growth factor receptor (EGFR) is one of the most extensively studied receptors exhibiting various lipid interactions, including interactions with phosphatidylcholine, phosphatidylserine, phosphatidylinositol phosphate, cholesterol, gangliosides, and palmitate. Here, we review recent findings on how direct interaction with these lipids regulates EGFR activation and signaling, providing unprecedented insight into the comprehensive roles of various lipids in the control of EGFR functions. Finally, the current limitations in investigating lipid-protein interactions and novel technologies to potentially overcome these limitations are discussed.

Integrated Omics Analysis of Non-Small-Cell Lung Cancer Cells Harboring the EGFR C797S Mutation Reveals the Potential of AXL as a Novel Therapeutic Target in TKI-Resistant Lung Cancer

Simple Summary

In this study, we employed CRISPR/Cas9 editing technology to introduce the EGFR C797S mutation into an NSCLC cell line harboring EGFR L858R/T790M to establish a cellular model for the investigation of the resistance mechanism associated with the acquired C797S mutation and to explore strategies to battle this type of TKI resistance. Transcriptome and proteome analyses revealed that the differentially expressed genes/proteins in the cells harboring the EGFR C797S mutation are associated with elevated expression of AXL. Furthermore, we presented evidence that inhibition of AXL is effective in slowing the growth of NSCLC cells harboring EGFR C797S. Our findings suggest that AXL inhibition could be a second-line or a potential adjuvant treatment for NSCLC harboring the EGFR C797S mutation.

Abstract

Oncogenic mutations of epidermal growth factor receptor (EGFR) are responsive to targeted tyrosine kinase inhibitor (TKI) treatment in non-small-cell lung cancer (NSCLC). However, NSCLC patients harboring activating EGFR mutations inevitably develop resistance to TKIs. The acquired EGFR C797S mutation is a known mechanism that confers resistance to third-generation EGFR TKIs such as AZD9291. In this work, we employed CRISPR/Cas9 genome-editing technology to knock-in the EGFR C797S mutation into an NSCLC cell line harboring EGFR L858R/T790M. The established cell model was used to investigate the biology and treatment strategy of acquired EGFR C797S mutations. Transcriptome and proteome analyses revealed that the differentially expressed genes/proteins in the cells harboring the EGFR C797S mutation are associated with a mesenchymal-like cell state with elevated expression of AXL receptor tyrosine kinase. Furthermore, we presented evidence that inhibition of AXL is effective in slowing the growth of NSCLC cells harboring EGFR C797S. Our findings suggest that AXL inhibition could be a second-line or a potential adjuvant treatment for NSCLC harboring the EGFR C797S mutation.