BPIFB3 interacts with ARFGAP1 and TMED9 to regulate non-canonical autophagy and RNA virus infection

TMED9: a potential therapeutic target and prognostic marker in glioma and its implications across pan-cancer contexts

Background

The escalating global cancer burden, projected to reach 35 million new cases by 2050, underscores the urgent need for innovative cancer biomarkers to improve treatment efficacy and patient outcomes. The TMED family, particularly TMED9, has garnered attention for its involvement in cancer progression; however, its comprehensive role across various cancer types remains poorly understood.

Methods

Utilizing multi-omics data, we analyzed the expression pattern, prognostic significance, genomic alterations, and immunological features of TMED9 in various cancer types. Through in vitro experiments, we paid special attention to its role in glioma, especially its correlation with glioma cell migration and invasion behavior.

Results

Our findings reveal that TMED9 is significantly overexpressed in various tumor tissues and is associated with poor prognosis in cancers such as glioblastoma and lower-grade gliomas. Genetic analysis shows TMED9 mutations predominantly in kidney renal clear cell carcinoma, with its expression linked to chromosomal instability. Immunological analysis indicates that TMED9 correlates positively with immune cell infiltration, particularly macrophages, suggesting its role in promoting tumor immunity. Furthermore, TMED9 expression was negatively correlated with tumor stemness, indicating its potential influence on chemotherapy resistance. Knockdown of TMED9 led to reduced migration and invasion in glioma cell lines.

Conclusions

Our comprehensive analysis positions TMED9 as a critical player in cancer progression and immune modulation, especially in gliomas. Elevated TMED9 expression correlates with poorer outcomes and may serve as a prognostic marker and therapeutic target. Future research should focus on elucidating TMED9's mechanistic pathways and validating its role in clinical settings to enhance glioma treatment strategies.

Mapping the Protein Phosphatase 1 Interactome in Human Cytomegalovirus Infection

Protein phosphorylation is a crucial regulatory mechanism in cellular homeostasis. The human cytomegalovirus (HCMV) incorporates protein phosphatase 1 (PP1) into its tegument, yet the biological relevance and mechanisms of this incorporation remain unclear. Our study offers the first characterization of the PP1 interactome during HCMV infection and its alterations. Using co-immunoprecipitation, mass spectrometry, and quantitative proteomics, we identified 159 high-confidence interacting proteins (HCIPs) in the PP1 interactome, consisting of 126 human and 33 viral proteins. We observed significant temporal changes in the PP1 interactome following HCMV infection, including the altered interactions of PP1 regulatory subunits. Further analysis highlighted the central roles of these PP1 interacting proteins in intracellular trafficking, with particular emphasis on the trafficking protein particle complex and Rab GTPases, which are crucial for the virus's manipulation of host cellular processes in virion assembly and egress. Additionally, our study on the noncatalytic PP1 inhibitor 1E7-03 revealed a decrease in PP1's interaction with key HCMV proteins, supporting its potential as an antiviral agent. Our findings suggest that PP1 docking motifs are critical in viral-host interactions and offer new insights for antiviral strategies.

Prognostic value and anti-tumor immunity role of TMED9 in pan-cancer: a bioinformatics study

Background

Transmembrane p24 trafficking protein 9 (TMED9) belongs to the TMED family, and its overexpression frequently induces cancer. Studies have demonstrated the association between the overexpression of TMED9 and cancer development and proliferative migration in cancers such as ovarian cancer, hepatocellular carcinoma, and breast cancer. However, there has been no study investigating the clinical value, biological function, and anti-tumor immune effects of TMED9 from a pan-cancer perspective. The aim of this study is to evaluate the prognostic value and anti-tumor immunity role of TMED9 across pan-cancers.

Methods

We utilized R language along with The Cancer Genome Atlas (TCGA), UCSC Xena (University of California, Santa Cruz Xena Browser), Human Protein Atlas (HPA), and other datasets to investigate TMED9 expression in various tumors. The association between high TMED9 expression and clinical prognosis and patient survival was examined using the Kaplan-Meier method, log-rank test, as well as univariate and multivariate Cox regression analyses. Tumor Immune Estimation Resource 2.0 (TIMER2.0) and various algorithms were employed to explore the relationship between TMED9 and the tumor microenvironment (TME). Additionally, the biological function of TMED9 in cancer was investigated through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) analyses.

Results

TMED9 was over-expressed in the majority of cancers. Patients exhibiting elevated TMED9 expression typically experienced diminished survival rates and unfavorable clinical outcomes. TMED9 played a role as a mediator in the aggressive phenotype of numerous tumors, actively engaging in various biological and signaling pathways linked to cancer development. TMED9 demonstrated the capacity to modulate the anti-tumor immune response in pan-cancer patients, exerting its influence on the infiltration levels of immune cells and cancer-associated fibroblasts (CAFs).

Conclusions

TMED9 serves as a novel "cancer indicator" and "clinical prognostic marker", capable of reshaping the TME, impacting the immunotherapeutic response, and guiding precise treatments for cancers to a certain extent.

The many hats of transmembrane emp24 domain protein TMED9 in secretory pathway homeostasis

The secretory pathway is an intracellular highway for the vesicular transport of newly synthesized proteins that spans the endoplasmic reticulum (ER), Golgi, lysosomes and the cell surface. A variety of cargo receptors, chaperones, and quality control proteins maintain the smooth flow of cargo along this route. Among these is vesicular transport protein TMED9, which belongs to the p24/transmembrane emp24 domain (TMED) family of proteins, and is expressed across vertebrate species. The TMED family is comprised of structurally-related type I transmembrane proteins with a luminal N-terminal Golgi-dynamics domain, a luminal coiled-coil domain, a transmembrane domain and a short cytosolic C-terminal tail that binds COPI and COPII coat proteins. TMED9, like other members of the TMED family, was first identified as an abundant constituent of the COPI and COPII coated vesicles that mediate traffic between the ER and the Golgi. TMED9 is typically purified in hetero-oligomers together with TMED family members, suggesting that it may function as part of a complex. Recently, TMED family members have been discovered to play various roles in secretory pathway homeostasis including secreted protein processing, quality control and degradation of misfolded proteins, and post-Golgi trafficking. In particular, TMED9 has been implicated in autophagy, lysosomal sorting, viral replication and cancer, which we will discuss in this Mini-Review.

Quantitative Proteomics Explore the Potential Targets and Action Mechanisms of Hydroxychloroquine

Hydroxychloroquine (HCQ) is an autophagy inhibitor that has been used for the treatment of many diseases, such as malaria, rheumatoid arthritis, systemic lupus erythematosus, and cancer. Despite the therapeutic advances in these diseases, the underlying mechanisms have not been well determined and hinder the rational use of this drug in the future. Here, we explored the possible mechanisms and identified the potential binding targets of HCQ by performing quantitative proteomics and thermal proteome profiling on MIA PaCa-2 cells. This study revealed that HCQ may exert its functions by targeting some autophagy-related proteins such as ribosyldihydronicotinamide dehydrogenase (NQO2) and transport protein Sec23A (SEC23A), or regulating the expression of galectin-8 (LGALS8), mitogen-activated protein kinase 8 (MAPK8), and so on. Furthermore, HCQ may prevent the progression of pancreatic cancer by regulating the expression of nesprin-2 (SYNE2), protein-S-isoprenylcysteine O-methyltransferase (ICMT), and cotranscriptional regulator FAM172A (FAM172A). Together, these findings not only identified potential binding targets for HCQ but also revealed the non-canonical mechanisms of HCQ that may contribute to pancreatic cancer treatment.

ER-Phagy and Microbial Infection

The endoplasmic reticulum (ER) is an essential organelle in cells that synthesizes, folds and modifies membrane and secretory proteins. It has a crucial role in cell survival and growth, thus requiring strict control of its quality and homeostasis. Autophagy of the ER fragments, termed ER-phagy or reticulophagy, is an essential mechanism responsible for ER quality control. It transports stress-damaged ER fragments as cargo into the lysosome for degradation to eliminate unfolded or misfolded protein aggregates and membrane lipids. ER-phagy can also function as a host defense mechanism when pathogens infect cells, and its deficiency facilitates viral infection. This review briefly describes the process and regulatory mechanisms of ER-phagy, and its function in host anti-microbial defense during infection.