A potential tumor marker: Chaperonin containing TCP‑1 controls the development of malignant tumors (Review)

Chaperonin containing TCP1 subunit 5 as a novel pan-cancer prognostic biomarker for tumor stemness and immunotherapy response: insights from multi-omics data, integrated machine learning, and experimental validation

BACKGROUND

Chaperonin containing TCP1 subunit 5 (CCT5), a vital component of the molecular chaperonin complex, has been implicated in tumorigenesis, cancer stemness maintenance, and therapeutic resistance. Nevertheless, its comprehensive roles in pan-cancer progression, underlying biological functions, and potential as a predictor of immunotherapy response remains poorly understood.

METHODS

We performed a comprehensive multi-omics pan-cancer analysis of CCT5 across 33 cancer types, integrating bulk RNA-seq, single-cell RNA-seq (scRNA-seq), and spatial transcriptomics data. CCT5 expression patterns, prognostic relevance, stemness association, and immune microenvironment relationships were evaluated. A novel CCT5-based signature (CCT5.Sig) was developed using machine learning on 23 immune checkpoint blockade (ICB) cohorts (n = 1394) spanning eight cancer types. Model performance was assessed using AUC metrics and survival analyses.

RESULTS

CCT5 was significantly overexpressed in tumor tissues and primarily localized to malignant and cycling cells. High CCT5 expression correlated with poor prognosis in multiple cancers and was enriched in oncogenic, cell cycle, and DNA damage repair pathways. CCT5 expression was positively associated with mRNAsi, mDNAsi, and CytoTRACE scores, indicating a role in stemness maintenance. Furthermore, CCT5-high tumors exhibited immune-cold phenotypes, with reduced TILs and CD8⁺ T cell activity. The CCT5.Sig model, based on genes co-expressed with CCT5, achieved superior predictive accuracy for ICB response (AUC = 0.82 in validation and 0.76 in independent testing), outperforming existing pan-cancer signatures.

CONCLUSION

This study reveals the multifaceted oncogenic roles of CCT5 and highlights its potential as a pan-cancer biomarker for prognosis and immunotherapy response. The machine learning-derived CCT5.Sig model provides a robust tool for patient stratification and may inform personalized immunotherapy strategies.

Pan-cancer analysis reveals immunological and prognostic significance of CCT5 in human tumors

The chaperonin containing TCP1 subunit 5 (CCT5) is believed to function as a tumor driver. However, a systematic pan-cancer analysis of CCT5 is still lacking. Therefore, this study aimed to identify the potential role of CCT5 in different types of tumors. This study comprehensively investigated the gene expression, proteomic expression, immune infiltration, DNA methylation, genetic alterations, correlation with TMB and MSI, drug sensitivity, enrichment analysis, and prognostic significance of CCT5 in 33 different tumors based on the TIMER2.0, GEPIA2, UALCAN, SMART, cBioPortal, GSCA databases, and TCGAplot R package. The results revealed significant CCT5 overexpression in most tumors and was significantly associated with poor OS and DFS in different tumor types. Reduced promoter and N-shore methylation of CCT5, indicating its potential oncogenic and epigenetic roles. Amplification was the most common type of CCT5 alterations. Immune infiltration analysis revealed a strong correlation between CCT5 and different immune cells. CCT5 exhibited a significant correlation with TMB and MSI in KIRC and STAD. Furthermore, enrichment analysis revealed associations between CCT5 and cell cycle pathway and various cellular functions. These findings suggested that CCT5 might serve as a potential prognostic biomarker and target for immunotherapy in various cancers.

AI-Driven Prediction of Cardio-Oncology Biomarkers Through Protein Corona Analysis

Protein corona, a layer predominantly composed of proteins and other biomolecules that forms on nanoparticle surfaces upon interaction with biological fluids, has recently been extensively utilized to enhance the depth of plasma proteomics and biomarker discovery. In this study, we integrate protein corona profiling with mass spectrometry (MS)-based bottom-up proteomics (BUP), machine learning, and causality analysis to identify potential biomarkers in the field of cardio-oncology. We selected prostate cancer (PC) and atherosclerosis as model cardio-oncology diseases, given that PC is the most prevalent cancer among men in the United States and frequently coexists with atherosclerotic cardiovascular disease (ASCVD), which contributes to the progression of metastatic PC (mPC). Protein corona profiles were generated from 35 plasma samples categorized into four groups: mPC with ASCVD, nonmetastatic PC (nmPC) with ASCVD, mPC without ASCVD, and nmPC without ASCVD. MS-based BUP analysis identified 887 unique proteins within the protein corona. Gene Ontology (GO) analysis of the 260 proteins common to all samples revealed key plasma proteomic pathways significantly associated with ASCVD and mPC. Using Least Absolute Shrinkage and Selection Operator (LASSO) regularization, we isolated 22 proteins strongly associated with ASCVD or mPC, including chaperonin containing TCP1 subunit 7 (CCT7), which was common to both conditions. Automated formal reasoning and causality analysis of these 22 proteins identified thromboxane-A synthase 1 (TBXAS1) as a primary causal factor linked to both ASCVD and mPC. TBXAS1 plays a critical role in promoting platelet aggregation, vascular smooth muscle cell proliferation, endothelial dysfunction, and thrombosis. In this proof-of-concept study, CCT7 and TBXAS1 emerged as potential biomarkers for both ASCVD and mPC, suggesting their utility as dual biomarkers for early detection and targeted therapeutic interventions. By combining nanomedicine with advanced analytical methods, our integrated approach provides a robust framework for uncovering causal relationships between biomarkers and disease states.

Comprehensive prediction and analysis of human protein essentiality based on a pretrained large language model

Human essential proteins (HEPs) are indispensable for individual viability and development. However, experimental methods to identify HEPs are often costly, time consuming and labor intensive. In addition, existing computational methods predict HEPs only at the cell line level, but HEPs vary across living human, cell line and animal models. Here we develop a sequence-based deep learning model, Protein Importance Calculator (PIC), by fine-tuning a pretrained protein language model. PIC not only substantially outperforms existing methods for predicting HEPs but also provides comprehensive prediction results across three levels: human, cell line and mouse. Furthermore, we define the protein essential score, derived from PIC, to quantify human protein essentiality and validate its effectiveness by a series of biological analyses. We also demonstrate the biomedical value of the protein essential score by identifying potential prognostic biomarkers for breast cancer and quantifying the essentiality of 617,462 human microproteins.

Advances in the study of CCT3 in malignant tumors: A review

Malignant tumors are among the leading causes of death worldwide, with their underlying mechanisms remaining largely unclear. Tumorigenesis is a complex process involving multiple factors, genes, and pathways. Tumor cells are characterized by abnormal proliferation, infiltration, invasion, and metastasis. Improving tumor diagnosis rates and identifying novel molecular therapeutic targets are of great significance for the advancement of modern medicine. Chaperonin containing TCP-1 subunit 3 (CCT3) is one of the subunits of the chaperonin containing TCP-1 complex, a molecular chaperone involved in protein folding and remodeling. CCT3 plays a crucial role in maintaining protein homeostasis, with key substrates including tubulin and actin. In recent years, CCT3 has been reported to be abnormally expressed in various cancers, correlating with prognosis and therapeutic outcomes. In this review, we summarize the basic structure and function of chaperonin containing TCP-1 complex and CCT3, and discuss the role of CCT3 in tumor development. Additionally, we explore its potential applications in cancer diagnosis and treatment.

Chaperonin containing TCP1 subunit 6A may activate Notch and Wnt pathways to facilitate the malignant behaviors and cancer stemness in oral squamous cell carcinoma

Chaperonin containing TCP1 subunit 6A (CCT6A) was recently discovered to be involved in cancer pathogenesis and stemness; however, its role in oral squamous cell carcinoma (OSCC) has not been reported. The current study aimed to investigate the impact of CCT6A on OSCC cell malignant behaviors and stemness and to explore its potentially interreacted pathways. SCC-15 and HSC-3 cells were transfected with the plasmid loading control overexpression, CCT6A overexpression, control knockout, or CCT6A knockout. Wnt4 overexpression or Notch1 overexpression plasmids were transfected into CCT6A-knockout SCC-15 cells. Cell proliferation, apoptosis, invasion, stemness, Notch, and Wnt pathways were detected in both cell lines, whereas RNA sequencing was only performed in SCC-15 cells. CCT6A was upregulated in five OSCC cell lines, including SCC-15, HSC-3, SAT, SCC-9, and KON, compared to that in the control cell line. In SCC-15 and HSC-3 cells, CCT6A overexpression increased cell proliferation, invasion, sphere formation, CD133, and Sox2 expression, but decreased cell apoptosis; on the contrary, CCT6A knockout exhibited an opposite effect on the above indexes. RNA-sequencing data revealed that the Wnt and Notch pathways were involved in the CCT6A'effect on SCC-15 cell functions. CCT6A positively regulates the Wnt and Notch pathways in SCC-15 and HSC-3 cells. Importantly, it was shown that activation of the Wnt or Notch pathways attenuated the effect of CCT6A knockout on SCC-15 cell survival, invasion, and stemness. CCT6A may promote OSCC malignant behavior and stemness by activating the Wnt and Notch pathways.

PANX2 promotes malignant transformation of colorectal cancer and 5-Fu resistance through PI3K-AKT signaling pathway

Colorectal cancer (CRC) is the third deadliest cancer in the world, with a high incidence, aggressiveness, poor prognosis, and resistant to drugs. 5-fluorouracil (5-FU) is the most commonly used drug for the chemotherapeutic of CRC, however, CRC is resistant to 5-FU after a period of treatment. Therefore, there is an urgent need to explore the underlying molecular mechanisms of CRC resistance to 5-FU. In the present study, we found that the expression of PANX2 was increased in CRC tissues and metastatic tissues from the TCGA database. The K-M survival curve showed that the high expression of PANX2 was associated with poor cancer prognosis. GDSC database showed that the IC50 of 5-Fu in the PANX2 high expression group was significantly higher, and the results were verified in CRC cells. In vitro cell function and in vivo tumorigenesis experiments showed that PANX2 promoted CRC cell proliferation, clone formation, migration and tumorigenesis in vivo. WB result revealed that PANX2 may lead to resistance to 5-Fu in CRC by affecting the PI3K-AKT signaling pathway. Overall, PANX2 regulates CRC proliferation, clone formation, migration, and 5-Fu resistance by PI3K-AKT signaling pathway.

METTL14-mediated N6-methyladenosine modification of TCP1 mRNA promotes acute myeloid leukemia progression

BACKGROUND

Acute myeloid leukemia (AML) is a prevalent hematologic malignancy characterized by a steady rise in morbidity and mortality rates over time. The upregulation of methyltransferase-like 14 (METTL14) expression in AML has been identified; however, its specific contributions to AML progression and underlying molecular mechanisms have yet to be elucidated.

METHOD

METTL14-bound mRNAs were predicted using bioinformatics methods, analyzed, and screened to identify T-complex protein 1 (TCP1). The regulatory impact of METTL14 on TCP1 was observed. TCP1 expression in AML clinical samples was assessed using quantitative real-time PCR and western blot analysis. The involvement of TCP1 in AML malignant progression was assessed through in vitro and in vivo functional assays. The String database was utilized for predicting proteins that interact with TCP1, while western blot assays and immunoprecipitation were employed to validate the associated signaling pathways.

RESULTS

METTL14 overexpression upregulates TCP1 expression in AML cells. AML patients exhibit high levels of TCP1 expression. Elevated TCP1 levels in HL60 and U937 cells in vitro lead to increased proliferation, migration, invasion, and inhibition of apoptosis, while in vivo, it accelerates AML proliferation and tumorigenesis. Mechanistically, METTL14 modulates AML progression by influencing TCP1 transcript stability via m6A methylation, thereby regulating TCP1 expression. Additionally, PPP2R2C potentially serves as a crucial functional target of TCP1 implicated in the malignant progression of AML.

CONCLUSION

Upregulation of TCP1 expression in AML through METTL14-mediated m6A modification accelerates the malignant progression of the disease. Therefore, targeting the m6A modification of TCP1 could be a potential therapeutic strategy to enhance the treatment of AML.

Development and Validation of an Interpretable Machine Learning Model for Early Prognosis Prediction in ICU Patients with Malignant Tumors and Hyperkalemia

This study aims to develop and validate a machine learning (ML) predictive model for assessing mortality in patients with malignant tumors and hyperkalemia (MTH). We extracted data on patients with MTH from the Medical Information Mart for Intensive Care-IV, version 2.2 (MIMIC-IV v2.2) database. The dataset was split into a training set (75%) and a validation set (25%). We used the Least Absolute Shrinkage and Selection Operator (LASSO) regression to identify potential predictors, which included clinical laboratory indicators and vital signs. Pearson correlation analysis tested the correlation between predictors. In-hospital death was the prediction target. The Area Under the Curve (AUC) and accuracy of the training and validation sets of 7 ML algorithms were compared, and the optimal 1 was selected to develop the model. The calibration curve was used to evaluate the prediction accuracy of the model further. SHapley Additive exPlanations (SHAP) and Local Interpretable Model-agnostic Explanations (LIME) enhanced model interpretability. 496 patients with MTH in the Intensive Care Unit (ICU) were included. After screening, 17 clinical features were included in the construction of the ML model, and the Pearson correlation coefficient was <0.8, indicating that the correlation between the clinical features was small. eXtreme Gradient Boosting (XGBoost) outperformed other algorithms, achieving perfect scores in the training set (accuracy: 1.000, AUC: 1.000) and high scores in the validation set (accuracy: 0.734, AUC: 0.733). The calibration curves indicated good predictive calibration of the model. SHAP analysis identified the top 8 predictive factors: urine output, mean heart rate, maximum urea nitrogen, minimum oxygen saturation, minimum mean blood pressure, maximum total bilirubin, mean respiratory rate, and minimum pH. In addition, SHAP and LIME performed in-depth individual case analyses. This study demonstrates the effectiveness of ML methods in predicting mortality risk in ICU patients with MTH. It highlights the importance of predictors like urine output and mean heart rate. SHAP and LIME significantly enhanced the model's interpretability.

Molecular Chaperonin HSP60: Current Understanding and Future Prospects

Molecular chaperones are highly conserved across evolution and play a crucial role in preserving protein homeostasis. The 60 kDa heat shock protein (HSP60), also referred to as chaperonin 60 (Cpn60), resides within mitochondria and is involved in maintaining the organelle's proteome integrity and homeostasis. The HSP60 family, encompassing Cpn60, plays diverse roles in cellular processes, including protein folding, cell signaling, and managing high-temperature stress. In prokaryotes, HSP60 is well understood as a GroEL/GroES complex, which forms a double-ring cavity and aids in protein folding. In eukaryotes, HSP60 is implicated in numerous biological functions, like facilitating the folding of native proteins and influencing disease and development processes. Notably, research highlights its critical involvement in sustaining oxidative stress and preserving mitochondrial integrity. HSP60 perturbation results in the loss of the mitochondria integrity and activates apoptosis. Currently, numerous clinical investigations are in progress to explore targeting HSP60 both in vivo and in vitro across various disease models. These studies aim to enhance our comprehension of disease mechanisms and potentially harness HSP60 as a therapeutic target for various conditions, including cancer, inflammatory disorders, and neurodegenerative diseases. This review delves into the diverse functions of HSP60 in regulating proteo-homeostasis, oxidative stress, ROS, apoptosis, and its implications in diseases like cancer and neurodegeneration.

Regulation of Epithelial and Endothelial Barriers by Molecular Chaperones

The integrity and permeability of epithelial and endothelial barriers depend on the formation of tight junctions, adherens junctions, and a junction-associated cytoskeleton. The establishment of this junction-cytoskeletal module relies on the correct folding and oligomerization of its protein components. Molecular chaperones are known regulators of protein folding and complex formation in different cellular compartments. Mammalian cells possess an elaborate chaperone network consisting of several hundred chaperones and co-chaperones. Only a small part of this network has been linked, however, to the regulation of intercellular adhesions, and the systematic analysis of chaperone functions at epithelial and endothelial barriers is lacking. This review describes the functions and mechanisms of the chaperone-assisted regulation of intercellular junctions. The major focus of this review is on heat shock protein chaperones, their co-chaperones, and chaperonins since these molecules are the focus of the majority of the articles published on the chaperone-mediated control of tissue barriers. This review discusses the roles of chaperones in the regulation of the steady-state integrity of epithelial and vascular barriers as well as the disruption of these barriers by pathogenic factors and extracellular stressors. Since cytoskeletal coupling is essential for junctional integrity and remodeling, chaperone-assisted assembly of the actomyosin cytoskeleton is also discussed.

Molecular Signatures Integral to Natural Reprogramming in the Pigment Epithelium Cells after Retinal Detachment in Pleurodeles waltl

The reprogramming of retinal pigment epithelium (RPE) cells into retinal cells (transdifferentiation) lies in the bases of retinal regeneration in several Urodela. The identification of the key genes involved in this process helps with looking for approaches to the prevention and treatment of RPE-related degenerative diseases of the human retina. The purpose of our study was to examine the transcriptome changes at initial stages of RPE cell reprogramming in adult newt Pleurodeles waltl. RPE was isolated from the eye samples of day 0, 4, and 7 after experimental surgical detachment of the neural retina and was used for a de novo transcriptome assembly through the RNA-Seq method. A total of 1019 transcripts corresponding to the differently expressed genes have been revealed in silico: the 83 increased the expression at an early stage, and 168 increased the expression at a late stage of RPE reprogramming. We have identified up-regulation of classical early response genes, chaperones and co-chaperones, genes involved in the regulation of protein biosynthesis, suppressors of oncogenes, and EMT-related genes. We revealed the growth in the proportion of down-regulated ribosomal and translation-associated genes. Our findings contribute to revealing the molecular mechanism of RPE reprogramming in Urodela.