High immune cytolytic activity in tumor-free tongue tissue confers better prognosis in patients with squamous cell carcinoma of the oral tongue

Immune Cytolytic Activity and Strategies for Therapeutic Treatment

Intratumoral immune cytolytic activity (CYT), calculated as the geometric mean of granzyme-A (GZMA) and perforin-1 (PRF1) expression, has emerged as a critical factor in cancer immunotherapy, with significant implications for patient prognosis and treatment outcomes. Immune checkpoint pathways, the composition of the tumor microenvironment (TME), antigen presentation, and metabolic pathways regulate CYT. Here, we describe the various methods with which we can assess CYT. The detection and analysis of tumor-infiltrating lymphocytes (TILs) using flow cytometry or immunohistochemistry provide important information about immune cell populations within the TME. Gene expression profiling and spatial analysis techniques, such as multiplex immunofluorescence and imaging mass cytometry allow the study of CYT in the context of the TME. We discuss the significant clinical implications that CYT has, as its increased levels are associated with positive clinical outcomes and a favorable prognosis. Moreover, CYT can be used as a prognostic biomarker and aid in patient stratification. Altering CYT through the different methods targeting it, offers promising paths for improving treatment responses. Overall, understanding and modulating CYT is critical for improving cancer immunotherapy. Research into CYT and the factors that influence it has the potential to transform cancer treatment and improve patient outcomes.

Construction of an enhanced computed tomography radiomics model for non-invasively predicting granzyme A in head and neck squamous cell carcinoma by machine learning

PURPOSE

Classical prognostic indicators of head and neck squamous cell carcinoma (HNSCC) can no longer meet the clinical needs of precision medicine. This study aimed to establish a radiomics model to predict Granzyme A (GZMA) expression in patients with HNSCC.

METHODS

We downloaded transcriptomic data of HNSCC patients from The Cancer Genome Atlas for prognosis analysis and then used corresponding enhanced computed tomography (CT) images from The Cancer Imaging Archive for feature extraction and model construction. We explored the influence of differences in GZMA expression on signaling pathways and analyzed the potential molecular mechanism and its relationship with immune cell infiltration. Subsequently, non-invasive CT radiomics models were established to predict the expression of GZMA mRNA and evaluate the correlation with the radiomics-score (Rad-score), related genes, and prognosis.

RESULTS

We found that GZMA was highly expressed in tumor tissues, and high GZMA expression was a protective factor for overall survival. The degree of B and T lymphocyte and natural killer cell infiltration was significantly correlated with GZMA expression. The receiver operating characteristic curve showed that the Relief GBM and RFE_GBM radiomics models had good predictive ability, and there were significant differences in the Rad-score distribution between the high- and low-GZMA-expression groups.

CONCLUSIONS

GZMA expression can significantly affect the prognosis of patients with HNSCC. Enhanced CT radiomics models can effectively predict the expression of GZMA mRNA.

Transcriptomic and Cellular Content Analysis of Colorectal Cancer by Combining Multiple Independent Cohorts

INTRODUCTION

By linking cellular content and molecular subtypes of colorectal cancer (CRC), we aim to uncover novel features useful for targeted therapy. Our first goal was to evaluate gene expression alterations linked to CRC pathogenesis, and then, we aimed to evaluate the cellular composition differences between normal colon mucosa and tumor and between different colon cancer molecular subtypes.

METHODS

We collected microarray and RNA sequencing data of patients with CRC from the Genome Expression Omnibus and The Cancer Genome Atlas. We combined all cases and performed quantile normalization. Genes with a fold change of >2 were further investigated. We used xCell for cellular decomposition and CMScaller for molecular subtyping. For statistical analyses, the Kruskal-Wallis H test and Mann-Whitney U tests were performed with Bonferroni correction.

RESULTS

We established an integrated database of normal colon and CRC using transcriptomic data of 1,082 samples. By using this data set, we identified genes showing the highest differential expression in colon tumors. The top genes were linked to calcium signaling, matrix metalloproteinases, and transcription factors. When compared with normal samples, CD4+ memory T cells, CD8+ naive T cells, CD8+ T cells, Th1 cells, Th2 cells, and regulatory T cells were enriched in tumor tissues. The ImmuneScore was decreased in tumor samples compared with normal samples. The CMS1 and CMS4 molecular subtypes were the most immunogenic, with the highest ImmuneScore but also high infiltration by CD8+ T cells, Th1 cells, and Th2 cells in CMS1 and B-cell subtypes and CD8+ T cells in CMS4.

DISCUSSION

Our analysis uncovers features enabling advanced treatment selection and the development of novel therapies in CRC.

A composite score based on immune-related gene prognostic index and m6A risk score of head and neck squamous cell carcinoma

Background: Immunotherapy has been demonstrated favorable in head and neck squamous cell carcinoma (HNSCC). Studies indicated that immune-related gene prognostic index (IRGPI) was a robust signature, and N⁶-methyladenosine (m⁶A) methylation had a significant impact on the tumor immune microenvironment (TIME) and immunotherapy of head and neck squamous cell carcinoma. Thus, combining indicated that immune-related gene prognostic index with m⁶A status should offer a better predictive power for immune responses. Methods: Head and neck squamous cell carcinoma samples from the cancer genome atlas (TCGA, n = 498) and gene expression omnibus database (GSE65858, n = 270) were used in this study. Cox regression analysis was used to construct the indicated that immune-related gene prognostic index through immune-related hub genes which were identified by weighted gene co-expression network analysis (WGCNA). The m⁶A risk score was constructed by least absolute shrinkage and selection operator (LASSO) regression analysis. Principal component analysis was used to construct a composite score, and systematically correlate subgroups according to tumor immune microenvironment cell-infiltrating characteristics. Results: A composite score was determined based on indicated that immune-related gene prognostic index and m⁶A risk score. Head and neck squamous cell carcinoma patients in the cancer genome atlas were divided into four subgroups: A (IRGPI-High&m⁶A-risk-High, n = 127), B (IRGPI-High&m⁶A-risk-Low, n = 99), C (IRGPI-Low&m⁶A-risk-High, n = 99), and D (IRGPI-Low&m⁶A-risk-Low, n = 128), and overall survival (OS) was significantly different between subgroups (p < 0.001). The characteristics of tumor immune microenvironment cell infiltration in the four subgroups were significantly different in subgroups (p < 0.05). The receiver operating characteristic (ROC) curves show the predictive value of composite score for overall survival was superior to other scores. Conclusion: The composite score is a promising prognostic signature which might distinguish immune and molecular characteristics, predict prognosis, and guide more effective immunotherapeutic strategies for head and neck squamous cell carcinoma.

m7G-related lncRNAs are potential biomarkers for predicting prognosis and immune responses in patients with oral squamous cell carcinoma

Among head and neck cancers, oral squamous cell carcinoma (OSCC) is the most common malignant tumor. N-7-methylguanosine (m7G) and lncRNAs are both related to the development and progression of tumors. Therefore, this study aims to explore and establish the prognostic signal of OSCC based on m7G-related lncRNAs. In this study, RNA sequencing transcriptome data of OSCC patients were downloaded from The Cancer Genome Atlas (TCGA) database. Therefore, m7G-related lncRNAs were identified as differentially expressed in OSCC. Then, univariate Cox regression analysis and LASSO regression analysis were conducted to evaluate the prognostic significance of differentially expressed lncRNAs. Consequently, the abovementioned lncRNAs were assigned five OSCC patient risk scores, with high-risk and low-risk patients assigned to each group. Different signaling pathways were significantly enriched between the two groups as determined by set enrichment analysis (GSEA). Multivariate Cox regression analysis confirmed the factors used to construct the nomogram model. Then, the prognosis of the nomogram model was evaluated. Consequently, high-risk individuals had higher immune infiltration levels. According to the results of a study that evaluated the sensitivity of different risk subgroups to antitumour drugs, the high-risk group had a high sensitivity to doxorubicin. By performing real-time polymerase chain reaction (RT‒PCR), we verified the expression of these five m7G lncRNAs. Therefore, the model based on five m7G-related lncRNAs was able to predict the overall survival rates of OSCC patients and guide their treatment. It can also spur new ideas about how to prevent and treat OSCC.

An oxidative stress-related prognostic signature for indicating the immune status of oral squamous cell carcinoma and guiding clinical treatment

Oral squamous cell carcinoma (OSCC) is the eighth most common cancer worldwide and presents high mortality. Oxidative stress, caused by reactive oxygen species accumulation, plays a crucial role in tumorigenesis, cancer progression, and drug resistance. Nevertheless, the specific prognostic and clinical values of oxidative stress-related genes (OSGs) in OSCC remain unclear. Here, we developed an oxidative stress-related prognostic signature according to mRNA expression data from The Cancer Genome Atlas (TCGA) database and evaluated its connections with the prognosis, clinical features, immune status, immunotherapy, and drug sensitivity of OSCC through a series of bioinformatics analyses. Finally, we filtered out six prognostic OSGs to construct a prognostic signature. On the basis of both TCGA-OSCC and GSE41613 cohorts, the signature was proven to be an independent prognostic factor with high accuracy and was confirmed to be an impactful indicator for predicting the prognosis and immune status of patients with OSCC. Additionally, we found that patients with high-risk scores may obtain greater benefit from immune checkpoint therapy compared to those with low-risk scores, and the risk score presented a close interaction with the tumor microenvironment and chemotherapy sensitivity. The prognostic signature may provide a valid and robust predictive tool that could predict the prognosis and immune status and guide clinicians to develop personalized therapeutic strategies for patients with OSCC.

A composite score based on immune-related gene prognostic index and m6A risk score of head and neck squamous cell carcinoma.. [DOI: 10.21203/rs.3.rs-1987322/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Background:Immunotherapy has been demonstrated favorable in head and neck squamous cell carcinoma (HNSCC). Studies indicated that immune-related gene prognostic index (IRGPI) was a robust signature, and N6-methyladenosine (m6A) methylation had a significant impact on the tumor immune microenvironment (TIME) and immunotherapy of HNSCC. Thus, combining IRGPI with m6A status should offer a better predictive power for immune responses.Methods:HNSCC samples from The Cancer Genome Atlas (TCGA, n=498) and Gene Expression Omnibus database (GSE65858, n = 270) were used in this study. Cox regression analysis was used to construct the IRGPI through immune-related hub genes which were identified by weighted gene co-expression network analysis (WGCNA). The m6A risk score was constructed by least absolute shrinkage and selection operator regression analysis. Principal component analysis was used to construct a composite score, and systematically correlate subgroups according to TIME cell-infiltrating characteristics.Results:A composite score was determined based on IRGPI and m6A risk score. HNSCC patients in the TCGA were divided into four subgroups：A (IRGPI-High&m6A-risk-High, n=127), B (IRGPI-High&m6A-risk-Low, n=99), C (IRGPI-Low&m6A-risk-High, n=99) and D (IRGPI-Low&m6A-risk-Low, n=128), and overall survival (OS) was significantly different between subgroups (P< 0.001). The characteristics of TIME cell infiltration in the four subgroups were significantly different in subgroups (P< 0.05). The ROC curves show the predictive value of composite score for OS was superior to any other scores.Conclusions:The composite score is a promising prognostic signature which might distinguish immune and molecular characteristics, predict prognosis, and guide more effective immunotherapeutic strategies for HNSCC.

Gene expression-based immune infiltration analyses of renal cancer and their associations with survival outcome

BACKGROUND

Renal cancer is a common malignant tumor with an increasing incidence rate.

METHODS

In this study, based on the gene expression profiles, we analyzed the compositions of tumor-infiltrating immune cells (TIICs) in renal cancer and paracancerous samples using CIBERSORT. The proportions of 22 TIICs subsets in 122 paired renal carcinoma and paracancerous samples, and 224 Wilms tumor (WT) samples varied between intragroup and intergroup.

RESULTS

After analyzed the difference of TIICs composition between renal cancer and paired paracancerous samples, we found that M0 macrophages and CD8 T cells were significantly elevated, while naive B cells were significantly decreased in renal cancer samples compared with paracancerous samples. Survival analysis showed that high overall TIICs proportion, the low proportion of resting mast cells and the high proportion of activated memory CD4 T cells were associated with poor prognosis of renal cancer patients. In addition, 3 clusters were identified by hierarchical clustering analysis, and they presented a distinct prognosis. Cluster 1 had superior survival outcomes, while cluster 2 had an inferior survival outcome.

CONCLUSIONS

Our study indicated that overall TIICs proportion, certain TIICs subset proportion, including resting mast cells and activated memory CD4 T cells, and distinct cluster patterns were associated with the prognosis of renal cancer, which was significant for the clinical surveillance and treatment of renal cancer.

Granzyme family acts as a predict biomarker in cutaneous melanoma and indicates more benefit from anti-PD-1 immunotherapy

The incidence of cutaneous melanoma (CM) increased since the 1970s, and also along with an unfavorable prognosis. CM patients have been verified benefits from immunotherapy, and granzymes (GZMs) comprise more than 90% of the cytolytic granules secreted by cytotoxic T lymphocytes and nature killer cell. Therefore, it is essential to evaluate the prognostic value of GZMs in CM. A total of 633 CM patients was enrolled to access the prognostic value of GZMs. The integrated prognostic value of five GZMs was validated in TCGA-SKCM, GSE65904, GSE53118, GSE19234 and GSE22153 cohorts. GZMscore, age, Breslow's depth and tumor stage are the independent risk factors for CM patients, risk score based on these factors was calculated in TCGA-SKCM and GSE65906 cohorts, which could polarize the CM patients to high- and low-risk groups with diverse prognosis. Patients in low-risk group obtained the activated immune signaling pathways and response, especially for the activated CD8+ T cells, and could benefit more from anti-PD-1 therapy. A higher tumor mutation burden was observed in low-risk group, especially for the mutation of BRAF. The protect function of GZMK was confirmed by CM cell lines, overexpression of GZMK in A375 and G361 cells suppresses cell proliferation, migration, but not cell apoptosis. All in all, we revealed the prognostic value of GZMs in CM patients, which could also act as a predicted value for the selection of responders of anti-PD-1 immunotherapy.

Transfer-RNA-Derived Fragments Are Potential Prognostic Factors in Patients with Squamous Cell Carcinoma of the Head and Neck

Transfer-RNA-derived fragments (tRFs) are a class of small non-coding RNAs that are functionally different from their parental transfer RNAs (tRNAs). tRFs can regulate gene expression by several mechanisms, and are involved in a variety of pathological processes. Here, we aimed at understanding the composition and abundance of tRFs in squamous cell carcinoma of the head and neck (SCCHN), and evaluated the potential of tRFs as prognostic markers in this cancer type. We obtained tRF expression data from The Cancer Genome Atlas (TCGA) HNSC cohort (523 patients) using MINTbase v2.0, and correlated to available TCGA clinical data. RNA-binding proteins were predicted according to the calculated Position Weight Matrix (PWM) score from the RNA-Binding Protein DataBase (RBPDB). A total of 10,158 tRFs were retrieved and a high diversity in expression levels was seen. Fifteen tRFs were found to be significantly associated with overall survival (Kaplan-Meier survival analysis, log rank test p-value < 0.01). The top prognostic marker, tRF-20-S998LO9D (p < 0.001), was further measured in tumor and tumor-free samples from 16 patients with squamous cell carcinoma of the oral tongue and 12 healthy controls, and was significantly upregulated in tumor compared to matched tumor-free tongue (p < 0.001). Results suggest that tRFs are useful prognostic markers in SCCHN.

Leukoplakia and Immunology: New Chemoprevention Landscapes?

Oral potentially malignant disorders (OPMDs) comprise a range of clinical-pathological alterations frequently characterized by an architectural and cytological derangements upon histological analysis. Among them, oral leukoplakia is the most common type of these disorders. This work aims to analyze the possible use of drugs such as immunochemopreventive agents for OPMDs. Chemoprevention is the use of synthetic or natural compounds for the reversal, suppression, or prevention of a premalignant lesion conversion to malignant form. Experimental and in vivo data offer us the promise of molecular prevention through immunomodulation; however, currently, there is no evidence for the efficacy of these drugs in the chemoprevention action. Alternative ways to deliver drugs, combined use of molecules with complementary antitumor activities, diet influence, and better definition of individual risk factors must also be considered to reduce toxicity, improve compliance to the protocol treatment and offer a better individualized prevention. In addition, we must carefully reconsider the mode of action of many traditional cancer chemoprevention agents on the immune system, such as enhancing immunosurveillance and reversing the immune evasion. Several studies emphasize the concept of green chemoprevention as an alternative approach to accent healthy lifestyle changes in order to decrease the incidence of HNSCC.

Downregulation of TAP1 in Tumor-Free Tongue Contralateral to Squamous Cell Carcinoma of the Oral Tongue, an Indicator of Better Survival

Oral cancers are surrounded by epithelium that histologically might seem normal, but genetically has aberrations. In patients with squamous cell carcinoma of the oral tongue (SCCOT), it is therefore important to study not only the tumor but also the clinically tumor-free contralateral tongue tissue that remains in the patient after treatment to map changes of prognostic and/or diagnostic value. The transporter associated with antigen processing (TAP) dimer is a key factor in the process of activating cytotoxic T cells. By downregulating the expression of TAP, tumor cells can escape cytotoxic T cell recognition. Biopsies from tumor and clinically tumor-free contralateral tongue tissue in 21 patients with SCCOT were analyzed together with tongue biopsies from 14 healthy individuals, which served as the control group. Dividing patients into TAP1-high and TAP1-low groups according to the median TAP1 level in tumor-free samples showed that patients with lower TAP1 mRNA levels in tumor-free samples had better overall (p = 0.003) and disease-free survival (p = 0.002). The results showing that TAP1 levels in tumor-free tongue tissue contralateral to the SCCOT correlate with survival is an important contribution to early diagnosis and follow up of SCCOT.

PD-L1 in squamous cell carcinoma of the oral tongue shows gender-specific association with prognosis

OBJECTIVE

To use alternative quantitation approaches to clarify the clinical implication of programmed cell death ligand 1 (PD-L1) in squamous cell carcinoma of the oral tongue (SCCOT).

MATERIALS AND METHODS

Ventana SP263 immunohistochemistry assay and a multiplicative QuickScore method were applied to quantify PD-L1 in tumor and surrounding immune cells from 101 patients with SCCOT. Tumor-infiltrating immune cells were estimated from bulk tissue transcriptional profiles of 25 patients. Circulating PD-L1 levels were measured in serum from 30 patients using an electrochemiluminescence assay platform.

RESULTS

We found higher tumor cell PD-L1 levels in females than males (p = .019). For patients with low PD-L1 in tumor cells, better survival was seen in males than females (overall survival p = .021, disease-free survival p = .020). Tumor-infiltrating natural killer T cells, immature dendritic cells, and M1 macrophages were positively associated with tumor cell PD-L1 (p < .05).

CONCLUSIONS

Our data confirmed the significance of gender on tumor cell PD-L1 expression and demonstrated combined effects of gender and PD-L1 levels on clinical outcome in patients with SCCOT. The data also indicated the involvement of specific immune cell types in PD-L1-regulated immune evasion.