The ryanodine receptor mutational characteristics and its indication for cancer prognosis

Low RYR2 Level Relates to Poor Prognosis of Patients With Lung Adenocarcinoma by Promoting Tumor Cell Proliferation and Inhibiting Immune Cell Infiltration

Ryanodine receptor type 2 (RYR2) is a large calcium channel that has been identified as one of the most frequently mutated genes in lung adenocarcinoma (LUAD). Despite its potential significance, the role of RYR2 in LUAD remains poorly understood. In this study, we obtained transcriptomic data (normal n = 59, tumor n = 541) from TCGA portal and RYR2 protein abundance data from cProSite, which includes 86 normal and 91 tumor samples. Additionally, we assembled a cohort of 38 patients with LUAD and collected paired tumor and adjacent non-tumor control samples. To investigate the functional impact of RYR2, we employed 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and flow cytometry analysis to assess cell viability and apoptosis, respectively. While mitochondria function was evaluated via measuring oxygen consumption rate. The relationship between RYR2 expression level and immune cell infiltration was analyzed by immunohistochemistry and flow cytometry analysis. Furthermore, RT-qPCR and enzyme-linked immunosorbent assay were used to quantify the expression levels of CCL14 and CXCL12. Our findings demonstrated that both the mRNA and protein levels of RYR2 were significantly downregulated in LUAD samples, and lower RYR2 levels are associated with the poor patient prognosis. Overexpression of RYR2 in A549 and H1299 cells resulted in impaired mitochondrial function, decreased cell viability, and increased apoptosis. Notably, RYR2 levels exhibited a negative correlation with tumor purity, and tumors with lower RYR2 levels showed diminished infiltration of T cells and dendritic cells. Knockdown of RYR2 in LUAD cells inhibited the production of chemokines, particularly CCL14 and CXCL12. In conclusion, our study reveals that RYR2 functions as a tumor suppressor in LUAD by inducing mitochondrial dysfunction and promoting immune cell infiltration.

Integrating multi-omics data reveals the antitumor role and clinical benefits of gamma-delta T cells in triple-negative breast cancer

BACKGROUND

Gamma-delta (γδ) T cells are a critical component of the tumor microenvironment and have been recognized as a promising biomarker and target for cancer therapy. Increasing evidence suggests that γδT cells play distinct roles in different cancers. However, the impact of γδT cells in breast cancer remains controversial.

METHODS

In this study, we investigated the role of γδT cells in breast cancer using a comprehensive approach, including bulk and single-cell sequencing, radiomics based on magnetic resonance imaging (MRI), genomic data, and immunohistochemistry. Single-cell RNA profiling was used to infer the potential lineage evolution of γδT cells and their interactions with other immune cells. Bulk RNA sequencing was included to uncover the heterogeneity in signaling pathways, as well as radiotherapy and immunotherapy responses, among patients with varying levels of γδT cell abundance. Genomic analysis was used to recognize the critical gene mutations with the infiltration of γδT cells. Immunohistochemistry was performed to validate the prognostic value of γδT cells in breast cancer patients. Lastly, radiomics was used to establish a correlation between the abundance of γδT cells and the features of MRI images.

RESULTS

The γδT cell infiltration was closely associated with favorable prognosis in triple-negative breast cancer (TNBC) but not in other subtypes of breast cancer. γδT cells may exert antitumor effects through intrinsic lineage evolution or interact with antigen-presenting cells through ligand-receptor pairs. Patients with a high γδT cell abundance may benefit more from chemotherapy or radiotherapy alone than their combination. Additionally, patients with a high γδT cell abundance were more likely to benefit from immunotherapy. Finally, we established a radiomic model based on dynamic contrast-enhanced-MRI, which indicated the potential for estimating the γδT cell abundance for patients with TNBC.

CONCLUSION

Our study provides novel insight and a theoretical basis for individualized therapy of patients with TNBC based on γδT cells.

Establishment and validation of predictive models by mutational and transcriptional factors for the prognosis of stage IV colorectal cancer patients with liver metastasis who undergo palliative surgery on primary tumors

Background

The prognostic factors at mutational and transcriptional levels are not clear for stage IV colorectal cancer (CRC) patients with liver metastasis who undergo primary cancer palliative surgery with post-surgical adjuvant therapy. We aimed to establish and validate models for predicting the prognosis of these patients by combining mutational, transcriptional and clinicopathological information.

Methods

Data of 45 stage IV CRC patients with liver metastasis were downloaded from the cBioportal database as the training cohort. Another 30 patients from our hospital were retrospectively recruited as the external validation cohort. Patients were followed up to 4,699 days (median: 823 days) and 2,380 days (median: 980 days) for the overall survival (OS) in the training and validation cohort, respectively. Patients were followed up to 4,699 days (median: 264 days) and 2,259 days (median: 272 days) for the progression-free survival (PFS) in the training and validation cohort, respectively. Tissue samples of the primary CRC were collected and sequenced. Data were analyzed and figures were plotted using the R software.

Results

The mutational and transcriptional alterations and their features were characterized. APC, TP53, TTN, KRAS and SYNE1 were genes with the highest mutational frequency. Significantly upregulated and downregulated genes can be found in transcription. Age, APC2 mutations, and ADRB1, ASTL, MRPL23-AS1 and PDZK1 transcription significantly stratified patient OS, while the KRAS, PTPRF, FREM2, and CLOCK mutations and LY6H, TMEM163, RFX8, ARHDGDIG, TECTA and MYEOV transcriptions significantly stratified patient PFS. Multivariate analyses identified age, APC2 mutations and ADRB1 transcription as independent risk factors for OS. KRAS and PTPRF mutations and RFX8 and MYEOV transcriptions were independent risk factors for PFS. The above independent risk factors were used to establish prediction models for OS and PFS. For the OS model, the 1-, 3- and 5-year area under the curve (AUC) reached 0.858, 0.774 and 0.907 in internal validation, and reached 0.810, 0.778 and 0.924 in external validation, respectively. For the PFS model, the 6 months, 1-year and 1.5-year AUC reached 0.950, 0.803 and 0.847 in internal validation, and reached 0.919, 0.949 and 0.944 in external validation, respectively.

Conclusions

The prognostic factors for stage IV CRC patients with liver metastasis were identified. Models for predicting the OS and PFS were successfully established and validated. The models may help to establish the personalized therapeutic strategies before treatment.

Genomic, transcriptomic, and T cell receptor profiling in stratifying response to first-line chemoradiotherapy or radiotherapy for esophageal squamous cell carcinoma

Introduction

Esophageal squamous cell carcinoma (ESCC) accounts for 80% of esophageal cancer (EC) worldwide. The molecular characteristics of locally advanced ESCC have been extensively studied.

Methods

In this study, we investigate the genomic and transcriptomic characteristics and try to provide the basic T-cell receptors (TCRs) dynamics and its genomic and transcriptome association during the radiochemotherapy of ESCC using multi-omics analysis.

Results

A total of 23 patients with pathologic diagnoses of locally advanced ESCC were enrolled. The median tumor mutational burden (TMB) of the 23 ESCC patients were 3.47 mutations/ Mb (mega-base). The TP53, RTK/RAS, and NOTCH pathways were concurrently prevalent in ESCC. Besides, some less prevalent pathways, including WNT and HIPPO pathways also exhibited superior frequencies in ESCC. Meantime, we found the immune-hot tumor had higher immune infiltration scores. The median TMB in the progression-free survival (PFS) low group was significantly higher than that in the PFS-high group. The chromosomal copy number variation (CNV) burden of the neutrophil-to-lymphocyte ratio (NLR)-high group appeared to be higher than that of the NLR-low group, and the StromalScore in the NLR-low group was significantly higher. Clonality score was significantly increased from pre-treat to post-treat and from on-treat to post-treat. Shannon index was significantly decreased from pre-treat to post-treat and from on-treat to posttreat. Richness was significantly decreased from pre-treat to post-treat.

Discussion

Multiomics analysis provided the basic TCRs dynamics and their genomic and transcriptome association during the radio-chemotherapy of 23 locally advanced ESCC in China, and provided a valuable insights into the heterogeneity and the tumor microenvironment and treatment responses. Meantimes, the identification of biomarkers and the exploration of their association with treatment outcomes could have important implications for clinical practice.

The Role of Ryanodine Receptor 2 Polymorphisms in Oral Squamous Cell Carcinoma Susceptibility and Clinicopathological Features

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide, and oral squamous cell carcinoma (OSCC) is one of the most common types. There is strong evidence that ryanodine receptor 2 (RYR2) plays an important role in different types of cancer according to previous studies. Its expression is associated with survival in patients with HNSCC, but it is unknown whether altered RYR2 expression contributes to tumorigenesis. Therefore, we examined how RYR2 polymorphisms affect OSCC susceptibility and clinicopathological characteristics. Five single nucleotide polymorphisms (SNPs) of RYR2, rs12594, rs16835904, rs2779359, rs3765097, and rs3820216, were analyzed in 562 cases of OSCC and 332 healthy controls using real-time PCR. We demonstrated that RYR2 SNP rs12594 was significantly different between the case and control groups, but this difference was not significant after adjusting for personal habits. In contrast, we found that different genotypes of SNP rs2779359 were significantly associated with the characteristics of clinical stage and tumor size in OSCC patients, according to the odds ratios and the adjusted odds ratios; specifically, patients with the T genotype had 1.477-fold (95% CI, 1.043 to 2.091; p = 0.028) and 1.533-fold (95% CI, 1.087-2.162; p = 0.015) increases in clinical stage and tumor size, respectively, compared with patients with the C allele. The results of our study, in which RYR2 SNPs associated with OSCC progression and development were examined for the first time, suggest that clinicopathological characteristics may alter OSCC susceptibility. Finally, RYR2 SNP rs2779359 not only plays a role in both the prognosis and diagnosis of oral cancer but is also likely an important predictive factor for recurrence, response to treatment, and medication toxicity.

Methylation signatures as biomarkers for non-invasive early detection of breast cancer: A systematic review of the literature

BACKGROUND

Early detection of breast cancer would help alleviate the burden of treatment for early-stage breast cancer and help patient prognosis. There is currently no established gene panel that utilizes the potential of DNA methylation as a molecular signature for the early detection of breast cancer. This systematic review aims to identify the optimal methylation biomarkers for a non-invasive liquid biopsy assay and the gaps in knowledge regarding biomarkers for early detection of breast cancer.

METHODS

Following the PRISMA-ScR method, Pubmed and Google Scholar was searched for publications related to methylation biomarkers in breast cancer over a five-year period. Eligible publications were mined for key data fields such as study aims, cohort demographics, types of breast cancer studied, technologies used, and outcomes. Data was analyzed to address the objectives of the review.

RESULTS

Literature search identified 112 studies of which based on eligibility criteria, 13 studies were included. 28 potential methylation gene targets were identified, of which 23 were methylated at the promoter region, 1 was methylated in the body of the gene and 4 were methylated at yet to be identified locations.

CONCLUSIONS

Our evaluation shows that at minimum APC, RASSFI, and FOXA1 genes would be a promising set of genes to start with for the early detection of breast cancer, based on the sensitivity and specificity outlined in the studies. Prospective studies are needed to optimize biomarkers for broader impact in early detection of breast cancer.

Multi-omics approach for identifying CNV-associated lncRNA signatures with prognostic value in prostate cancer

BACKGROUND

Prostate cancer, the second most prevalent malignancy among men, poses a significant threat to affected patients' well-being due to its poor prognosis. Novel biomarkers are required to enhance clinical outcomes and tailor personalized treatments. Herein, we describe our research to explore the prognostic value of long non-coding RNAs (lncRNAs) deregulated by copy number variations (CNVs) in prostate cancer.

METHODS

The study employed an integrative multi-omics data analysis of the prostate cancer transcriptomic, CNV and methylation datasets to identify prognosis-related subtypes. Subtype-specific expression profiles of protein-coding genes (PCGs) and lncRNAs were determined. We analysed CNV patterns of lncRNAs across the genome to identify subtype-specific lncRNAs with CNV changes. LncRNAs exhibiting significant amplification or deletion and a positive correlation were designated CNV-deregulated lncRNAs. A prognostic risk score model was subsequently developed using these CNV-driven lncRNAs.

RESULTS

Six molecular subtypes of prostate cancer were identified, demonstrating significant differences in prognosis (P = 0.034). The CNV profiles of subtype-specific lncRNAs were examined, revealing their correlation with CNV amplification or deletion. Six lncRNAs (CCAT2, LINC01593, LINC00276, GACAT2, LINC00457, LINC01343) were selected based on significant CNV amplifications or deletions using a rigorous univariate Cox proportional risk regression model. A robust risk score model was developed, stratifying patients into high-risk and low-risk categories. Notably, our prognostic model based on these six lncRNAs exhibited exceptional predictive capabilities for recurrence-free survival (RFS) in prostate cancer patients (P = 0.024).

CONCLUSIONS

Our study successfully identified a prognostic risk score model comprising six CNV-driven lncRNAs that could potentially be prognostic biomarkers for prostate cancer. These lncRNA signatures are closely associated with RFS, providing promising prospects for improved patient prognostication and personalized therapeutic strategies for novel prostate cancer treatment.

Comprehensive Multiomics Analyses Establish the Optimal Prognostic Model for Resectable Gastric Cancer : Prognosis Prediction for Resectable GC

BACKGROUND

Prognostic models based on multiomics data may provide better predictive capability than those established at the single-omics level. Here we aimed to establish a prognostic model for resectable gastric cancer (GC) with multiomics information involving mutational, copy number, transcriptional, methylation, and clinicopathological alterations.

PATIENTS AND METHODS

The mutational, copy number, transcriptional, methylation data of 268, 265, 226, and 252 patients with stages I-III GC were downloaded from the TCGA database, respectively. Alterations from all omics were characterized, and prognostic models were established at the individual omics level and optimized at the multiomics level. All models were validated with a cohort of 99 patients with stages I-III GC.

RESULTS

TTN, TP53, and MUC16 were among the genes with the highest mutational frequency, while UBR5, ZFHX4, PREX2, and ARID1A exhibited the most prominent copy number variations (CNVs). Upregulated COL10A1, CST1, and HOXC10 and downregulated GAST represented the biggest transcriptional alterations. Aberrant methylation of some well-known genes was revealed, including CLDN18, NDRG4, and SDC2. Many alterations were found to predict the patient prognosis by univariate analysis, while four mutant genes, two CNVs, five transcriptionally altered genes, and seven aberrantly methylated genes were identified as independent risk factors in multivariate analysis. Prognostic models at the single-omics level were established with these alterations, and optimized combination of selected alterations with clinicopathological factors was used to establish a final multiomics model. All single-omics models and the final multiomics model were validated by an independent cohort. The optimal area under the curve (AUC) was 0.73, 0.71, 0.71, and 0.85 for mutational, CNV, transcriptional, and methylation models, respectively. The final multiomics model significantly increased the AUC to 0.92 (P < 0.05).

CONCLUSIONS

Multiomics model exhibited significantly better capability in predicting the prognosis of resectable GC than single-omics models.

RYR2 receptor gene mutation associated with catecholaminergic polymorphic ventricular tachycardia in children: a case report & literature review

Background

Ryanodine receptor 2 (RYR2) gene mutation causing catecholaminergic polymorphic ventricular tachycardia (CPVT) is one of the identified causes of sudden death in adults and children.

Case Description

We report a case of RYR2 gene mutation presented with cardiac arrest and recurrent syncopal attack with accidental finding of cardiac tumour. For the systematic review, we used four databases (Scopus, PubMed, Ovid and Google Scholar) to search articles with the terms "RYR2 gene mutation" and "catecholaminergic polymorphic ventricular tachycardia (CPVT)". Fourteen studies were chosen and reviewed together with our reported patient. Most of the patients presented initially with syncopal attack and developed cardiac arrest later. Some of them presented with both syncopal attack and seizures precipitated by exercise or stress. We found that 43.8% of patients shared similar variants or coding effects in RYR2 gene mutation. Demographically, the mean age at presentation is 11 years old with 53% of reported cases were male.

Conclusions

Refractory arrhythmias cardiac arrest not responding to adrenaline should raise the suspicion towards RYR2 gene mutations. Recognition of this condition is important as it affects the outcome of resuscitation. Untimely diagnosis of RYR2 gene mutations with appropriate use of pharmacological agents during resuscitation is important to ensure a better outcome.

Rhabdomyosarcoma Associated with Core Myopathy/Malignant Hyperthermia: Combined Effect of Germline Variants in RYR1 and ASPSCR1 May Play a Role

Rhabdomyosarcomas have been described in association with thyroid disease, dermatomyositis, Duchenne muscular dystrophy, and in muscular dystrophy models but not in patients with ryanodine receptor-1 gene (RYR1) pathogenic variants. We described here an 18-year-old male who reported a cervical nodule. Magnetic resonance images revealed a mass in the ethmoidal sinus corresponding to rhabdomyosarcoma. As his father died from malignant hyperthermia (MH), an in vitro contracture test was conducted and was positive for MH susceptibility. Muscle histopathological analysis in the biopsy showed the presence of cores. Molecular analysis using NGS sequencing identified germline variants in the RYR1 and ASPSCR1 (alveolar soft part sarcoma) genes. This report expands the spectrum of diseases associated with rhabdomyosarcomas and a possible differential diagnosis of soft tissue tumors in patients with RYR1 variants.

Mechanism of cis-Nerolidol-Induced Bladder Carcinoma Cell Death

Nerolidol is a naturally occurring sesquiterpene alcohol with multiple properties, including antioxidant, antibacterial, and antiparasitic activities. A few studies investigating the antitumor properties of nerolidol have shown positive results in both cell culture and mouse models. In this study, we investigated the antitumor mechanism of cis-nerolidol in bladder carcinoma cell lines. The results of our experiments on two bladder carcinoma cell lines revealed that nerolidol inhibited cell proliferation and induced two distinct cell death pathways. We confirmed that cis-nerolidol induces DNA damage and ER stress. A mechanistic study identified a common cAMP, Ca²⁺, and MAPK axis involved in signal propagation and amplification, leading to ER stress. Inhibition of any part of this signaling cascade prevented both cell death pathways. The two cell death mechanisms can be distinguished by the involvement of caspases. The early occurring cell death pathway is characterized by membrane blebbing and cell swelling followed by membrane rupture, which can be prevented by the inhibition of caspase activation. In the late cell death pathway, which was found to be caspase-independent, cytoplasmic vacuolization and changes in cell shape were observed. cis-Nerolidol shows promising antitumor activity through an unorthodox mechanism of action that could help target resistant forms of malignancies, such as bladder cancer.