p53 mutation and deletion contribute to tumor immune evasion

The search for a TNBC vaccine: the guardian vaccine

Nearly 20 million people are diagnosed with cancer each year with breast cancer being the most common among women. Triple negative breast cancer (TNBC), defined by its no/low expression of ER and PR and lack of amplification of HER2, makes up 15-20% of all breast cancer cases. While patients overall have a higher response to chemotherapy, this subgroup is associated with the lowest survival rate indicating significant clinical and molecular heterogeneity demanding alternate treatment options. Therefore, new therapies have been explored, with a large focus on utilizing the immune system. A whole host of immunotherapies have been studied including immune checkpoint inhibitors, now standard of care for eligible patients, and possibly the most exciting and promising is that of a TNBC vaccine. While currently there are no approved TNBC vaccines, this review highlights many promising studies and points to an antigen, p53, which we believe is highly relevant for TNBC.

TP53 Mutations and Phosphatidylinositol 3-Kinase/AKT Pathway Alterations Are Key Determinants of Breast Cancer Outcome Independent of Subtype and Stage

PURPOSE

Breast cancer (BC) is a heterogeneous disease with genetic alterations influencing prognosis and treatment response. TP53 mutations (TP53muts) are present in approximately 30% of BC, but their prognostic impact remains controversial. In addition, the phosphatidylinositol 3-kinase (PI3K)/Ak strain transforming (AKT) pathway is frequently altered and represents a promising therapeutic target for BC. Understanding the combined prognostic impact of TP53mut and PI3K/AKT pathway alterations across BC subtypes remains underexplored.

METHODS

This retrospective cohort study integrated clinical and genomic data from 4,265 patients with BC from the Molecular Taxonomy of Breast Cancer International Consortium (n = 2,509) and the Memorial Sloan Kettering Cancer Center (n = 1,756). Genetic profiling identified TP53mut and PI3K/AKT pathway alterations (AKT1, AKT2, AKT3, PIK3CA, PTEN, RICTOR). Survival outcomes were assessed using Kaplan-Meier survival analysis and multivariable Cox proportional hazards models.

RESULTS

In 3,807 patients with available gene alteration status, TP53mut was associated with younger age, higher tumor grade, advanced stage, and aggressive subtypes (P < .001). TP53mut was associated with worse survival independent of subtype, stage, age, and grade (hazard ratio [HR], 1.43 [95% CI, 1.24 to 1.66]; P < .0001). The type of TP53mut has also been found to be prognostic in BC. PI3K/AKT pathway alterations were more frequent in TP53mut tumors and independently associated with worse survival (HR, 1.18 [95% CI, 1.03 to 1.35]; P = .0173). The combined presence of TP53mut and PI3K/AKT alterations resulted in the worst survival outcomes (HR, 1.61 [95% CI, 1.32 to 1.97]; P < .0001).

CONCLUSION

TP53mut status is a critical prognostic factor in BC, independent of subtypes and stage, and its adverse impact is amplified by PI3K/AKT pathway alterations. These findings emphasize the integration of genetic profiling into routine clinical practice to refine treatment strategies and identify potential therapeutic targets for this high-risk population.

p53: A player in the tumor microenvironment

Approximately half of all cancers have p53 inactivating mutations, in addition to which most malignancies inactivate the p53 pathway by increasing p53 inhibitors, decreasing p53 activators, or inactivating p53 downstream targets. A growing number of researches have demonstrated that p53 can influence tumor progression through the tumor microenvironment (TME). TME is involved in the process of tumor development and metastasis and affects the clinical prognosis of patients. p53 participates in host immunity and engages in the immune landscape of the TME, but the specific mechanisms remain to be investigated. This review briefly explores the interactions between different states of p53 and TME components and their mechanisms, as well as their effects on tumor progression. To understand the progress of drug development and clinical studies related to p53 and tumor microenvironment.

AI Model for Predicting Anti-PD1 Response in Melanoma Using Multi-Omics Biomarkers

BACKGROUND

Immune checkpoint inhibitors (ICIs) have demonstrated significantly improved clinical efficacy in a minority of patients with advanced melanoma, whereas non-responders potentially suffer from severe side effects and delays in other treatment options. Predicting the response to anti-PD1 treatment in melanoma remains a challenge because the current FDA-approved gold standard, the nonsynonymous tumor mutation burden (nsTMB), offers limited accuracy.

METHODS

In this study, we developed a multi-omics-based machine learning model that integrates genomic and transcriptomic biomarkers to predict the response to anti-PD1 treatment in patients with advanced melanoma. We employed least absolute shrinkage and selection operator (LASSO) regression with 49 biomarkers extracted from tumor-normal whole-exome and RNA sequencing as input features. The performance of the multi-omics AI model was thoroughly compared to that of nsTMB alone and to models that use only genomic or transcriptomic biomarkers.

RESULTS

We used publicly available DNA and RNA-seq datasets of melanoma patients for the training and validation of our model, forming a meta-cohort of 449 patients for which the outcome was recorded as a RECIST score. The model substantially improved the prediction of anti-PD1 outcomes compared to nsTMB alone, with an ROC AUC of 0.7 in the training set and an ROC AUC of 0.64 in the test set. Using SHAP values, we demonstrated the explainability of the model's predictions on a per-sample basis.

CONCLUSIONS

We demonstrated that models using only RNA-seq or multi-omics biomarkers outperformed nsTMB in predicting the response of melanoma patients to ICI. Furthermore, our machine learning approach improves clinical usability by providing explanations of its predictions on a per-patient basis. Our findings underscore the utility of multi-omics data for selecting patients for treatment with anti-PD1 drugs. However, to train clinical-grade AI models for routine applications, prospective studies collecting larger melanoma cohorts with consistent application of exome and RNA sequencing are required.

Mapping the functional network of human cancer through machine learning and pan-cancer proteogenomics

Large-scale omics profiling has uncovered a vast array of somatic mutations and cancer-associated proteins, posing substantial challenges for their functional interpretation. Here we present a network-based approach centered on FunMap, a pan-cancer functional network constructed using supervised machine learning on extensive proteomics and RNA sequencing data from 1,194 individuals spanning 11 cancer types. Comprising 10,525 protein-coding genes, FunMap connects functionally associated genes with unprecedented precision, surpassing traditional protein-protein interaction maps. Network analysis identifies functional protein modules, reveals a hierarchical structure linked to cancer hallmarks and clinical phenotypes, provides deeper insights into established cancer drivers and predicts functions for understudied cancer-associated proteins. Additionally, applying graph-neural-network-based deep learning to FunMap uncovers drivers with low mutation frequency. This study establishes FunMap as a powerful and unbiased tool for interpreting somatic mutations and understudied proteins, with broad implications for advancing cancer biology and informing therapeutic strategies.

Long-term survival in a patient with Li-Fraumeni syndrome-associated giant cell glioblastoma treated with nivolumab: illustrative case

BACKGROUND

Li-Fraumeni syndrome (LFS) is characterized by p53 germline mutations and a high predisposition to cancers including glioblastoma (GBM), the most common and aggressive primary malignant brain tumor in adults. Despite current therapies, the 5-year survival rate is 5%-10%. The authors report a case with a durable long-term response to immunotherapy with checkpoint inhibition in a patient with LFS-associated GBM.

OBSERVATIONS

An 18-year-old female presented after a syncopal episode and left leg weakness and was found to have a right frontal tumor. She underwent gross-total resection of the tumor (grade IV giant cell GBM IDH-wildtype, MGMT unmethylated, associated with a p53 germline mutation), radiation, and chemotherapy. On later imaging, increased enhancement was demonstrated, which raised concerns for tumor recurrence, and she underwent stereotactic radiosurgery followed by lomustine and procarbazine. These agents were later replaced with bevacizumab after a second resection, negative for recurrent glioma. Subsequently, nivolumab was added, given concerns for tumor progression, and the patient showed improvement within 5 months. The patient has continued nivolumab monotherapy and has had progression-free survival for more than 7 years.

LESSONS

Despite advances in treatment, the median survival of patients with GBM is only 15 months. This case highlights the potential of immunotherapy with PD-L1 checkpoint inhibition in improving outcomes for LFS-associated GBM patients. https://thejns.org/doi/10.3171/CASE24539.

CCT6A functions as promising diagnostic biomarker and promotes cell proliferation in colorectal cancer

Background: Chaperonin-containing tailless complex polypeptide 1 subunit 6A (CCT6A) is mainly located in the cytoplasm and considered to be involved in various biological processes in tumors. However, its function and the intrinsic mechanism need to be further elucidated. Methods: Multi-omics analysis was used to evaluate the correlation between CCT6A expression and prognosis of patients, as well as its immune value. CCT6A was knockout by CRISPR-Cas9, and overexpressed by transfecting plasmids in colorectal cancer (CRC) cells. Cell proliferation was analyzed by MTS, EDU staining and colony growth assay, and cell migration was monitored by wound healing assay and Transwell assay. The phosphor-kinase array kit and immunoblotting assay was utilized to explore the potential molecular mechanisms. Results: CCT6A was highly expressed in multiple tumor tissues and significantly correlated with the prognosis of patients. It was also associated with the immune infiltration, immune correlation and prognosis in CRC. CCT6A was highly expressed in CRC biopsies as well as fresh CRC tissues. Meanwhile, knockout of CCT6A reduced cell proliferation, cell cycle and cell migration. On the contrary, overexpression of CCT6A exhibited the opposite phenotypes. Moreover, we identified that HSPD1 and non-phosphorylated P53 were highly increased in CCT6A overexpressed cells, which are involved in regulating tumorigenesis. Conclusions: Therefore, CCT6A positively regulated cell proliferation/migration in CRC cells, and suggesting CCT6A has a high immunological value and is associated with CRC progression, which makes it a potential therapeutic target for CRC.

Assessment of the Circulating PD-1 and PD-L1 Levels and P53 Expression as a Predictor of Relapse in Pediatric Patients with Wilms Tumor and Hypernephroma

Background/Objectives: Wilms tumor (WT) is the most common form of pediatric renal tumor, accounting for over 90% of cases followed by hypernephroma. Some pediatric patients with WT (10%) experience relapse or metastasis and have poor survival rates. PD-L1 assists cancer cells in escaping damage from the immune system. P53 mutations are found in relapsed WT tumor samples. We hypothesized that testing circulating PD-1 and PD-L1 and P53 expression levels could offer a simple method to predict patient relapse and explore novel treatments for pediatric WTs and hypernephroma. Methods: Flow cytometric detection of cPD-1, cPD-L1, and P53 expression in relapsed and in-remission WT and hypernephroma before and after one year of chemotherapy was performed. Results: Our data shows increased levels of cPD-L1 in relapsed pediatric patients with WT or hypernephroma before and after chemotherapy. There were also slight and significant increases in cPD-1 levels in relapsed groups before chemotherapy. Additionally, we observed significant decreases in P53 expression after one year of chemotherapy in relapsed pediatric patients. Conclusions: Our study found that circulating PD-L1 can be used as a predictor marker for WT and hypernephroma relapse. In conclusion, these circulating markers can assist in monitoring relapse in WT and hypernephroma patients without the need for several biopsies.

P53: A key player in diverse cellular processes including nuclear stress and ribosome biogenesis, highlighting potential therapeutic compounds

The tumor suppressor proteins are key transcription factors involved in the regulation of various cellular processes, such as apoptosis, DNA repair, cell cycle, senescence, and metabolism. The tumor suppressor protein p53 responds to different type of stress signaling, such as hypoxia, DNA damage, nutrient deprivation, oncogene activation, by activating or repressing the expression of different genes that target processes mentioned earlier. p53 has the ability to modulate the activity of many other proteins and signaling pathway through protein-protein interaction, post-translational modifications, or non-coding RNAs. In many cancers the p53 is found to be mutated or inactivated, resulting in the loss of its tumor suppressor function and acquisition of new oncogenic properties. The tumor suppressor protein p53 also plays a role in the development of other metabolic disorders such as diabetes, obesity, and fatty liver disease. In this review, we will summarize the current data and knowledge on the molecular mechanisms and the functions of p53 in different pathways and processes at the cellular level and discuss the its implications for human health and disease.

Dendritic cell-related hub genes in head-and-neck squamous cell carcinoma: implications for prognosis and immunotherapy

Background

In the context of head-and-neck squamous cell carcinoma (HNSCC), dendritic cells (DCs) assume pivotal responsibilities, acting as architects of antigen presentation and conductors of immune checkpoint modulation. In this study, we aimed to identify hub genes associated with DCs in HNSCC and explore their prognostic significance and implications for immunotherapy.

Methods

Integrated clinical datasets from The Cancer Genome Atlas (TCGA)-HNSCC and GSE65858 cohorts underwent meticulous analysis. Employing weighted gene co-expression network analysis (WGCNA), we delineated candidate genes pertinent to DCs. Through the application of random survival forest and least absolute shrinkage and selection operator (LASSO) Cox's regression, we derived key genes of significance. Lisa (epigenetic Landscape In Silico deletion Analysis and the second descendent of MARGE) highlighted transcription factors, with Dual-luciferase assays confirming their regulatory role. Furthermore, immunotherapeutic sensitivity was assessed utilizing the Tumor Immune Dysfunction and Exclusion online tool.

Results

This study illuminated the functional intricacies of HNSCC DC subsets to tailor innovative therapeutic strategies. We leveraged clinical data from the TCGA-HNSCC and GSE65858 cohorts. We subjected the data to advanced analysis, including WGCNA, which revealed 222 DC-related candidate genes. Following this, a discerning approach utilizing random survival forest analysis and LASSO Cox's regression unveiled seven genes associated with the prognostic impact of DCs, notably ACP2 and CPVL, associated with poor overall survival. Differential gene expression analysis between ACP2 + and ACP2 - DC cells revealed 208 differential expressed genes. Lisa analysis identified the top five significant transcription factors as STAT1, SPI1, SMAD1, CEBPB, and IRF1. The correlation between STAT1 and ACP2 was confirmed through quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Dual-luciferase assays in HEK293T cells. Additionally, TP53 and FAT1 mutations were more common in high-risk DC subgroups. Importantly, the sensitivity to immunotherapy differed among the risk clusters. The low-risk cohorts were anticipated to exhibit favorable responses to immunotherapy, marked by heightened expressions of immune system-related markers. In contrast, the high-risk group displayed augmented proportions of immunosuppressive cells, suggesting a less conducive environment for immunotherapeutic interventions.

Conclusions

Our research may yield a robust DC-based prognostic system for HNSCC; this will aid personalized treatment and improve clinical outcomes as the battle against this challenging cancer continues.

In-depth analysis of the interplay between oncogenic mutations and NK cell-mediated cancer surveillance in solid tumors

Natural killer (NK) cells play a crucial role in antitumoral and antiviral responses. Yet, cancer cells can alter themselves or the microenvironment through the secretion of cytokines or other factors, hindering NK cell activation and promoting a less cytotoxic phenotype. These resistance mechanisms, often referred to as the "hallmarks of cancer" are significantly influenced by the activation of oncogenes, impacting most, if not all, of the described hallmarks. Along with oncogenes, other types of genes, the tumor suppressor genes are frequently mutated or modified during cancer. Traditionally, these genes have been associated with uncontrollable tumor growth and apoptosis resistance. Recent evidence suggests oncogenic mutations extend beyond modulating cell death/proliferation programs, influencing cancer immunosurveillance. While T cells have been more studied, the results obtained highlight NK cells as emerging key protagonists for enhancing tumor cell elimination by modulating oncogenic activity. A few recent studies highlight the crucial role of oncogenic mutations in NK cell-mediated cancer recognition, impacting angiogenesis, stress ligands, and signaling balance within the tumor microenvironment. This review will critically examine recent discoveries correlating oncogenic mutations to NK cell-mediated cancer immunosurveillance, a relatively underexplored area, particularly in the era dominated by immune checkpoint inhibitors and CAR-T cells. Building on these insights, we will explore opportunities to improve NK cell-based immunotherapies, which are increasingly recognized as promising alternatives for treating low-antigenic tumors, offering significant advantages in terms of safety and manufacturing suitability.

Molecular mechanisms and therapeutic applications of huaier in breast cancer treatment

Breast cancer is one of the most common female malignant tumors today and represents a serious health risk for women. Although the survival rate and quality of life of patients with breast cancer are improving with the continuous development of medical technology, metastasis, recurrence, and drug resistance of breast cancer remain a significant problem. Huaier, a traditional Chinese medicine (TCM) fungus, is a type of Sophora embolism fungus growing on old Sophora stems. The polysaccharides of Trametes robiniophila Murr (PS-T) are the main active ingredient of Huaier. There is increasing evidence that Huaier has great potential in breast cancer treatment, and its anti-cancer mechanism may be related to a variety of biological activities, such as the inhibition of cell proliferation, metastasis, tumor angiogenesis, the promotion of cancer cell death, and regulation of tumor-specific immunity. There is growing evidence that Huaier may be effective in the clinical treatment of breast cancer. This review systematically summarizes the basic and clinical studies on the use of Huaier in the treatment of breast cancer, providing useful information to guide the clinical application of Huaier and future clinical studies.