Methods to Investigate EGFR Ubiquitination

Multidimensional Analysis of CHMP Family Members in Hepatocellular Carcinoma

Background

EGFR frequently accumulates and mutates simultaneously in various cancers. Ubiquitinated EGFR proteins can be degraded by the endosomal sorting complex required for transport. Among them, ESCRTIII is mainly composed of CHMP family members.

Methods

A total of 424 samples from the TCGA-LIHC data set were used to explore the relationship between CHMPs and liver hepatocellular carcinoma (LIHC). Oncomine, the Human Protein Altas, cBioPortal, TISIDB, TIMER, Metascape, and R software were used to facilitate analysis of the role played by CHMPs in the pathogenesis of LIHC. The role of CHMPs in the development of LIHC was analyzed in terms of differential expression, survival, mutation, immunoinfiltration, functional enrichment, and drug sensitivity.

Results

Differential expression analysis showed that CHMPs were significantly more expressed in LIHC tumor tissue, and the high expression of some CHMPs was closely correlated with clinicopathological stage. The prognosis was worse in the group with high expression of CHMPs. Among them, CHMP4C was considered to play a major role. Gene-mutation analysis and DNA promoter–methylation analysis further revealed possible mechanisms for the aberrant amplification of CHMPs. Immunoinfiltration analysis indicated that CHMPs were closely associated with multiple immune cells and exhibited resistance to various drugs when highly expressed.

Conclusion

CHMPs were found to be significantly elevated in LIHC and strongly associated with immune-cell infiltration, poor prognosis, multiple star pathways, and drug resistance.

Western Blot Processing Optimization: The Perfect Blot

Western blot processing is a well-established procedure that includes protein extraction from tissues and cells, gel electrophoresis separation, transfer to a membrane, and immunodetection with specific antibodies. Here, we show that optimization of washing helps to maximize the specific interactions of antigens and antibodies. Performing all washing steps at 4 °C ensures a maximal signal to noise ratio and reduces nonspecific signals.

DaHuangWan targets EGF signaling to inhibit the proliferation of hepatoma cells

DaHuangWan (DHW) is a traditional herbal medicine used by Mongolian to treat liver cancer for many years. Clinical application of the drug has been shown to help control tumor progression, prolong survival and improve quality of life. However, the underlying mechanisms and side effects of this drug remain unclear, which greatly limits the clinical application and further optimization of DHW. In this study, we found that DHW inhibits the proliferation of hepatoma cells by modulating the epithelial growth factor (EGF) signaling pathway. Berberine and Costunolide are the main active ingredients in DHW. Interestingly, the combination of Berberine and Costunolide has a dramatic synergistic effect on inhibiting the proliferation of hepatoma cells. Neither Berberine nor Costunolide directly block EGFR phosphorylation. Berberine promotes endocytosis of activated EGFR, while as Costunolide increases ubiquitination of EGFR and reduces EGFR recycling to cell membrane distribution, thereby inhibiting EGF signaling. Berberine and Costunolide target two different steps in regulating the EGF signaling, which explains the synergistic anti-cancer effect of DHW. Since Berberine and Costunolide do not directly target EGFR phosphorylation, DHW could be a supplementary medicine to tyrosine kinase inhibitors in cancer therapy.

ELISA Based Protein Ubiquitylation Measurement

Ubiquitylation is a common post-translational modification of cellular proteins that results in proteasomal and lysosomal degradations. Ubiquitylation is generally measured by methods such as immunoblotting using anti-ubiquitin antibodies after isolating the protein-of-interest by denaturing immunoprecipitation. The following protocol can be used to easily quantify the ubiquitylation of the protein-of-interest tagged with biotin by ELISA.

Molecularly Distinct Clathrin-Coated Pits Differentially Impact EGFR Fate and Signaling

Adaptor protein 2 (AP2) is a major constituent of clathrin-coated pits (CCPs). Whether it is essential for all forms of clathrin-mediated endocytosis (CME) in mammalian cells is an open issue. Here, we demonstrate, by live TIRF microscopy, the existence of a subclass of relatively short-lived CCPs lacking AP2 under physiological, unperturbed conditions. This subclass is retained in AP2-knockout cells and is able to support the internalization of epidermal growth factor receptor (EGFR) but not of transferrin receptor (TfR). The AP2-independent internalization mechanism relies on the endocytic adaptors eps15, eps15L1, and epsin1. The absence of AP2 impairs the recycling of the EGFR to the cell surface, thereby augmenting its degradation. Accordingly, under conditions of AP2 ablation, we detected dampening of EGFR-dependent AKT signaling and cell migration, arguing that distinct classes of CCPs could provide specialized functions in regulating EGFR recycling and signaling.