SYT12 plays a critical role in oral cancer and may be a novel therapeutic target

Integration of bioinformatics and cellular experiments unveils the role of SYT12 in gastric cancer

OBJECTIVE

This study employs integrated bioinformatics analysis and in vitro cellular experiments to elucidate the role of Synaptotagmin-12 (SYT12) in the progression of gastric cancer.

METHODS

We utilized databases and platforms such as Xiantao Academic Tools, UALCAN, Kaplan-Meier plotter analysis, and The Cancer Genome Atlas (TCGA) to extract datasets on SYT12 in gastric cancer. We analyzed the relationship between SYT12 expression and the clinicopathological features, prognosis, diagnosis, and immune infiltration of stomach adenocarcinoma (STAD) patients. Verification was conducted using samples from 31 gastric cancer patients. Additionally, in vitro cellular experiments were performed to determine the role and potential mechanisms of SYT12 in the malignant behavior of gastric cancer cells.

RESULTS

Comprehensive bioinformatics analysis indicated that SYT12 is highly expressed in most cancers and is associated with promoter DeoxyriboNucleic Acid (DNA) methylation levels. SYT12 expression correlated with clinicopathological features, immune cell infiltration, immune checkpoint gene expression, and poor prognosis in STAD patients. In vitro experiments suggest that SYT12 may promote the proliferation and migration of gastric cancer cells by inducing epithelial-mesenchymal transition (EMT).

CONCLUSIONS

This study highlights the significant role of SYT12 in gastric cancer, suggesting its potential as a new target for early diagnosis, treatment, immunological, and prognostic evaluation in gastric cancer, offering new insights for precision medicine in this disease.

Establishment and assessment of an oral squamous cell carcinoma N7-methylguanosine methyltransferase associated microRNA prognostic model

Background: N7-methylguanosine (m7G) methyltransferases and microRNAs (miRNAs) are closely associated with tumor progression. However, the role of m7G methyltransferase-related miRNAs as prognostic markers in oral squamous cell carcinoma (OSCC) has not been studied. This study aimed to explore the m7G methyltransferase-related miRNAs in OSCC, establish a prognostic model based on m7G methyltransferase-related miRNAs, investigate their correlation with immune cell infiltration, and assess their potential prognostic value. Methods: Transcriptional and clinical data of patients with OSCC were obtained from The Cancer Genome Atlas (TCGA) database. TargetScan and miRWalk were used to predict m7G methyltransferase-related miRNAs. Subsequently, differentially expressed m7G methyltransferase-related miRNAs in TCGA-OSCC were selected. Cox and least absolute shrinkage and selection operator (LASSO) regression analyses were used to build an m7G methyltransferase-related miRNA risk prognostic model for TCGA-OSCC. Patients were stratified into high- and low-risk groups. The predictive and diagnostic accuracies of the risk prognostic model were further validated using Kaplan-Meier survival analysis, receiver operating characteristic (ROC) curve analysis, independent prognosis analysis, and nomogram plots. Finally, quantitative real-time polymerase chain reaction (qPCR) was used to validate the expression levels of m7G methyltransferase-related miRNAs in postoperative cancer and adjacent normal tissues from 60 patients with OSCC. Results: Through Cox and LASSO regression analysis, six candidate miRNAs (hsa-miR-338-3p, hsa-miR-1251-3p, hsa-miR-3129-5p, hsa-miR-4633-3p, hsa-miR-216a-3p, and hsa-miR-6503-3p) most relevant to the prognosis of patients with OSCC were identified to construct an m7G methyltransferase-related miRNA risk prognostic model. In this model, the overall survival (OS) of the high-risk group was significantly shorter than that of the low-risk group (P < 0.001). The model effectively predicted prognosis and served as an independent prognostic indicator for patients with OSCC. Compared with the low-risk group, the high-risk group exhibited a significantly increased capacity for immune cell infiltration (P < 0.05), while the activation and initiation abilities of immune cells were decreased. Finally, six m7G methyltransferase-related miRNAs were validated in OSCC tissue samples. Conclusion: The risk prognostic model based on six m7G methyltransferase-related miRNAs can predict the OS rate of patients with OSCC and has the potential to guide individualized treatment. This prognostic model is closely associated with immune cell infiltration in patients with OSCC.

A prognostic model built on amino acid metabolism patterns in HPV-associated head and neck squamous cell carcinoma

OBJECTIVES

To compare amino acid metabolism patterns between HPV-positive and HPV-negative head and neck squamous cell carcinoma (HNSCC) patients and identify key genes for a prognostic model.

DESIGN

Utilizing the Cancer Genome Atlas dataset, we analyzed amino acid metabolism genes, differentiated genes between HPV statuses, and selected key genes via LASSO regression for the prognostic model. The model's gene expression was verified through immunohistochemistry in clinical samples. Functional enrichment and CIBERSORTx analyses explored biological functions, molecular mechanisms, and immune cell correlations. The model's prognostic capability was assessed using nomograms, calibration, and decision curve analysis.

RESULTS

We identified 1157 key genes associated with amino acid metabolism in HNSCC and HPV status. The prognostic model, featuring genes like IQCN, SLC22A1, SYT12, and TLX3, highlighted functions in development, metabolism, and pathways related to receptors and enzymes. It significantly correlated with immune cell infiltration and outperformed traditional staging in prognosis prediction, despite immunohistochemistry results showing limited clinical identification of HPV-related HNSCC.

CONCLUSIONS

Distinct amino acid metabolism patterns differentiate HPV-positive from negative HNSCC patients, underscoring the prognostic model's utility in predicting outcomes and guiding therapeutic strategies.

Correlations of m6A Methylation-Related lncRNAs with the Prognosis of Papillary Thyroid Carcinoma

Purpose

Papillary thyroid carcinoma (PTC) is the most common subtype of thyroid cancer. Recurrence makes the prognosis for some patients with PTC worse. Increasing evidence have suggested that N6-methyladenosine (m6A) RNA methylation plays an important role in tumorigenesis. However, the significance of m6A-related lncRNAs in the malignant progression of PTC remains unknown. In this study, we explored the significance of M6A-related lncrnas in the malignant progression of PTC.

Patients and Methods

Transcriptome and clinical data of PTC were achieved and integrated from The Cancer Genome Atlas (TCGA). Firstly, a Spearman correlation analysis was performed to obtain m6A RNA methylation-associated lncRNAs. Next, We constructed a prognostic signature and assessed the accuracy of the signature by receiver operating characteristic (ROC) curve and Kaplan Meier survival analyses. Furthermore, functional enrichment analysis was performed on the high- and low-risk groups. Finally, we determined prognostic gene expression in clinical samples using quantitative reverse transcription polymerase chain reaction (RT-qPCR).

Results

We identified 56 differentially expressed lncRNAs associated with m6A RNA methylation. Univariate Cox and Least Absolute Shrinkage and Selection Operator (LASSO) regression analyses showed that the survival-related lncRNAs associated with m6A RNA methylation were detected, which showed superior calibration and discrimination. Moreover, the biological processes related to energy metabolism were significantly activated in the high-risk group. Finally, the co-expressed genes of lncRNAs in the risk model were significantly enriched in biological processes related to copper ion response. Finally, we validated the expression levels of three prognostic genes in clinical samples using RT-qPCR.

Conclusion

Our study revealed m6A RNA methylation-associated lncRNAs were significantly associated with disease-free survival in patients with papillary thyroid cancer, which would improve our understanding of the relationship between m6A RNA methylation-associated lncRNAs and PTC.

Machine learning algorithm integrates bulk and single-cell transcriptome sequencing to reveal immune-related personalized therapy prediction features for pancreatic cancer

Pancreatic cancer (PC) is a digestive malignancy with worse overall survival. Tumor immune environment (TIME) alters the progression and proliferation of various solid tumors. Hence, we aimed to detect the TIME-related classifier to facilitate the personalized treatment of PC. Based on the 1612 immune-related genes (IRGs), we classified patients into Immune_rich and Immune_desert subgroups via consensus clustering. Patients in distinct subtypes exhibited a difference in sensitivity to immune checkpoint blockers (ICB). Next, the immune-related signature (IRS) model was established based on 8 IRGs (SYT12, TNNT1, TRIM46, SMPD3, ANLN, AFF3, CXCL9 and RP1L1) and validated its predictive efficiency in multiple cohorts. RT-qPCR experiments demonstrated the differential expression of 8 IRGs between tumor and normal cell lines. Patients who gained lower IRS score tended to be more sensitive to chemotherapy and immunotherapy, and obtained better overall survival compared to those with higher IRS scores. Moreover, scRNA-seq analysis revealed that fibroblast and ductal cells might affect malignant tumor cells via MIF-(CD74+CD44) and SPP1-CD44 axis. Eventually, we identified eight therapeutic targets and one agent for IRS high patients. Our study screened out the specific regulation pattern of TIME in PC, and shed light on the precise treatment of PC.

Chromosome-level genome assembly and population genomics of Mongolian racerunner (Eremias argus) provide insights into high-altitude adaptation in lizards

BACKGROUND

Although the extreme environmental adaptation of organisms is a hot topic in evolutionary biology, genetic adaptation to high-altitude environment remains poorly characterized in ectothermic animals. Squamates are among the most diverse terrestrial vertebrates, with tremendous ecological plasticity and karyotype diversity, and are a unique model system to investigate the genetic footprints of adaptation.

RESULTS

We report the first chromosome-level assembly of the Mongolian racerunner (Eremias argus) and our comparative genomics analyses found that multiple chromosome fissions/fusions events are unique to lizards. We further sequenced the genomes of 61 Mongolian racerunner individuals that were collected from altitudes ranging from ~ 80 to ~ 2600 m above sea level (m.a.s.l.). Population genomic analyses revealed many novel genomic regions under strong selective sweeps in populations endemic to high altitudes. Genes embedded in those genomic regions are mainly associated with energy metabolism and DNA damage repair pathways. Moreover, we identified and validated two substitutions of PHF14 that may enhance the lizards' tolerance to hypoxia at high altitudes.

CONCLUSIONS

Our study reveals the molecular mechanism of high-altitude adaptation in ectothermic animal using lizard as a research subject and provides a high-quality lizard genomic resource for future research.

Potential roles of synaptotagmin family members in cancers: Recent advances and prospects

With the continuous development of bioinformatics and public database, more and more genes that play a role in cancers have been discovered. Synaptotagmins (SYTs) are abundant, evolutionarily conserved integral membrane proteins composed of a short N-terminus, a variable linker domain, a single transmembrane domain, and two C2 domains, and they constitute a family of 17 isoforms. The synaptotagmin family members are known to regulate calcium-dependent membrane fusion events. Some SYTs play roles in hormone secretion or neurotransmitter release or both, and much evidence supports SYTs as Ca²⁺ sensors of exocytosis. Since 5 years ago, an increasing number of studies have found that SYTs also played important roles in the occurrence and development of lung cancer, gastric cancer, colon cancer, and other cancers. Down-regulation of SYTs inhibited cell proliferation, migration, and invasion of cancer cells, but promoted cell apoptosis. Growth of peritoneal nodules is inhibited and survival is prolonged in mice administrated with siSYTs intraperitoneally. Therefore, most studies have found SYTs serve as an oncogene after overexpression and may become potential prognostic biomarkers for multiple cancers. This article provides an overview of recent studies that focus on SYT family members’ roles in cancers and highlights the advances that have been achieved.

Tumor Suppressive Circular RNA-102450: Development of a Novel Diagnostic Procedure for Lymph Node Metastasis from Oral Cancer

Circular RNAs (circRNAs), which form as covalently closed loop structures, have several biological functions such as regulation of cellular behavior by adsorbing microRNAs. However, there is limited information of circRNAs in oral squamous cell carcinoma (OSCC). Here, we aimed to elucidate the roles of aberrantly expressed circRNAs in OSCC. CircRNA microarray showed that circRNA-102450 was down-regulated in OSCC cells. Clinical validation of circRNA-102450 was performed using highly sensitive droplet digital PCR in preoperative liquid biopsy samples from 30 OSCC patients. Interestingly, none of 16 studied patients with high circRNA-102450 had regional lymph node metastasis (RLNM), whereas 4 of 14 studied patients (28.5%) with low expression had pathologically proven RLNM. Overexpressed circRNA-102450 significantly inhibited the tumor metastatic properties of cell proliferation, migration, and invasion. Furthermore, circRNA-102450 directly bound to, and consequently down-regulated, miR-1178 in OSCC cells. Taken together, circRNA-102450 has a tumor suppressive effect via the circRNA-102450/miR-1178 axis and may be a novel potential marker of RLNM in OSCC patients.

SYT12 is a novel oncogene that promotes thyroid carcinoma progression and metastasis

Background: Thyroid malignancy is the most frequent endocrine malignant tumor whose incidence is still increasing. Mechanisms genomic variations play a major part in the pathogenesis of many types of malignancy. Synaptotagmin 12 (SYT12) is a member gene of the synaptotagmins family and SYT12's variants were shown to be associated with some malignancies. Nevertheless, SYT12's specific function and probable clinical value in papillary cancer were still unknown. Methods: We conducted complete genome sequence of 39 pairs PTC malignant neoplasm and matched non-neoplastic tissues. We found that SYT12 was significantly overexpressed in thyroid malignancy. Next, we investigated the expression level of SYT12 and the relation between clinical information and SYT12 expression in thyroid cancer in the Cancer Genome Atlas (TCGA). QRt-PCR of else 40 pairs local verified cohort was performed to confirm the sequencing data and TCGA cohort. Then, we used small interfering RNA (si-RNA) to knock down the expression of SYT12 in PTC cells. Finally, proliferation, cell colony formation, migration, invasion, and apoptosis assays were done to demonstrate the function of SYT12. Results: SYT12 is significantly overexpressed and higher expression of SYT12 upsurges the risk of lymph node metastatic and incidence rate of primary neoplasm multivariate focus type and classical histological type for PTC patients in TCGA cohort. In vitro experiments, the results of functional assays presented that knock-down of SYT12 inhibited the cell proliferation, cell colony formation, trans-well migration, and trans-well invasion and promoted cell apoptotic in PTC cell lines. Conclusion: SYT12 was a novel oncogene that promotes thyroid carcinoma progression and metastasis potential and a potential biomarker for diagnosis and treatment in PTC.

The dysregulated expression and functional effect of CaMK2 in cancer

CaMK2 (calcium/calmodulin-dependent protein kinase 2), a multifunctional serine/threonine-protein kinase involved in diverse cellular processes, is vital for the transduction of the Ca²⁺ signaling cascade. Recently, research has highlighted the involvement of CaMK2 in cancer development. However, the specific effects of CaMK2 on cancer have not been fully elucidated. In this review, we summarize not only the altered expression of CaMK2 in a range of cancers, as evidenced by bioinformatics analysis, but also the significant role of CaMK2 in regulating cancer progression, such as proliferation and metastasis. In addition, we described the functional influence of CaMK2 on cancer stemness and resistance. Understanding the critical effects and mechanisms of CaMK2 in cancer would facilitate the development of a promising therapeutic strategy for cancer treatment.