Clusterin transcript variants expression in thyroid tumor: a potential marker of malignancy?

Single-Cell RNA Sequencing Revealed a 3-Gene Panel Predicted the Diagnosis and Prognosis of Thyroid Papillary Carcinoma and Associated With Tumor Immune Microenvironment

Objective

The objective of this research was to screen prognostic related genes of thyroid papillary carcinoma (PTC) by single-cell RNA sequencing (scRNA-seq), to construct the diagnostic and prognostic models based on The Cancer Genome Atlas Thyroid Cancer (TCGA-THCA) data, and to evaluate the association between tumor immune microenvironment and the prognostic model.

Method

The differentially expressed genes (DEGs) and tumor evolution were analyzed by scRNA-seq based on public databases. The potential regulatory networks of DEGs related to prognosis were analyzed by multi-omics data in the THCA. Logistic regression and Cox proportional hazards regression were utilized to construct the diagnosis and prognostic model of PTC. The performance of the diagnostic model was verified by bulk RNA sequencing (RNA-seq) of our cohort. The tumor immune microenvironment associated with the prognostic model was evaluated using multi-omics data. In addition, qRT-PCR was performed on tumor tissues and adjacent normal tissues of 20 patients to verify the expression levels of DEGs.

Results

The DEGs screened by scRNA-seq can distinguish between tumor and healthy samples. DEGs play different roles in the evolution from normal epithelial cells to malignant cells. Three DEGs ((FN1, CLU, and ANXA1)) related to prognosis were filtered, which may be regulated by DNA methylation, RNA methylation (m6A) and upstream transcription factors. The area under curve (AUC) of the diagnostic model based on 3-gene in the validation of our RNA-seq was 1. In the prognostic model based on 3-gene, the overall survival (OS) of high-risk patients was shorter. Combined with the clinical information of patients, a nomogram was constructed by using tumor size (pT) and risk score to quantify the prognostic risk. The age and tumor size of high-risk patients in the prognostic model were greater. In addition, the increase of tumor mutation burden (TMB) and diversity of T cell receptor (TCR), and the decrease of CD8⁺ T cells in high-risk group suggest the existence of immunosuppressive microenvironment.

Conclusion

We applied the scRNA-seq pipeline to focus on epithelial cells in PTC, simulated the process of tumor evolution, and revealed a prognostic prediction model based on 3 genes, which is related to tumor immune microenvironment.

Prognostic biomarkers for predicting papillary thyroid carcinoma patients at high risk using nine genes of apoptotic pathway

Aberrant expressions of apoptotic genes have been associated with papillary thyroid carcinoma (PTC) in the past, however, their prognostic role and utility as biomarkers remains poorly understood. In this study, we analysed 505 PTC patients by employing Cox-PH regression techniques, prognostic index models and machine learning methods to elucidate the relationship between overall survival (OS) of PTC patients and 165 apoptosis related genes. It was observed that nine genes (ANXA1, TGFBR3, CLU, PSEN1, TNFRSF12A, GPX4, TIMP3, LEF1, BNIP3L) showed significant association with OS of PTC patients. Five out of nine genes were found to be positively correlated with OS of the patients, while the remaining four genes were negatively correlated. These genes were used for developing risk prediction models, which can be utilized to classify patients with a higher risk of death from the patients which have a good prognosis. Our voting-based model achieved highest performance (HR = 41.59, p = 3.36x10^-4, C = 0.84, logrank-p = 3.8x10^-8). The performance of voting-based model improved significantly when we used the age of patients with prognostic biomarker genes and achieved HR = 57.04 with p = 10⁻⁴ (C = 0.88, logrank-p = 1.44x10^-9). We also developed classification models that can classify high risk patients (survival ≤ 6 years) and low risk patients (survival > 6 years). Our best model achieved AUROC of 0.92. Further, the expression pattern of the prognostic genes was verified at mRNA level, which showed their differential expression between normal and PTC samples. Also, the immunostaining results from HPA validated these findings. Since these genes can also be used as potential therapeutic targets in PTC, we also identified potential drug molecules which could modulate their expression profile. The study briefly revealed the key prognostic biomarker genes in the apoptotic pathway whose altered expression is associated with PTC progression and aggressiveness. In addition to this, risk assessment models proposed here can help in efficient management of PTC patients.

Comprehensive Identification of Potential Crucial Genes and miRNA-mRNA Regulatory Networks in Papillary Thyroid Cancer

Background

Thyroid cancer is the most common endocrine malignancy, with a recent global increase of 20% in age-related incidence. Ultrasonography and ultrasonography-guided fine-needle aspiration biopsy (FNAB) are the most widely used diagnostic tests for thyroid nodules; however, it is estimated that up to 25% of thyroid biopsies are cytologically inconclusive. Molecular markers can help guide patient-oriented and targeted treatment of thyroid nodules and thyroid cancer.

Methods

Datasets related to papillary thyroid cancer (PTC) or thyroid carcinoma (GSE129562, GSE3678, GSE54958, GSE138042, and GSE124653) were downloaded from the GEO database and analysed using the Limma package of R software. For functional enrichment analysis, the Kyoto Encyclopedia of Genes and Genomes pathway analysis and Gene Ontology were applied to differentially expressed genes (DEGs) using the Metascape website. A protein-protein interaction (PPI) network was built from the STRING database. Gene expression, protein expression, immunohistochemistry, and potential functional gene survival were analysed using the GEPIA website, the Human Protein Atlas website, and the UALCAN website. Potential target miRNAs were predicted using the miRDB and Starbase datasets.

Results

We found 219 upregulated and 310 downregulated DEGs, with a cut-off of p < 0.01 and ∣log FC | >1.5. The DEGs in papillary thyroid cancer were mainly enriched in extracellular structural organisation. At the intersection of the PPI network and Metascape MCODEs, the hub genes in common were identified as FN1, APOE, CLU, and SDC2. In the targeted regulation network of miRNA-mRNA, the hsa-miR-424-5p was found to synchronously modulate two hub genes. Survival analysis showed that patients with high expression of CLU and APOE had better prognosis.

Conclusions

CLU and APOE are involved in the molecular mechanism of papillary thyroid cancer. The hsa-miR-424-5p might have the potential to reverse the processes of papillary thyroid cancer by modulating the hub genes. These are potential targets for the treatment of patients with papillary thyroid cancer.

CCNA1 gene as a potential diagnostic marker in papillary thyroid cancer

The malignancy that most affects the endocrine system is thyroid neoplasm, with an increasing incidence over the years. The most prevalent histological type of the carcinomas that affect the thyroid gland is papillary carcinoma with a prevalence of 80 % worldwide. The current diagnostic methodology may present inconclusive results, emphasizing the need for new effective and sensitive techniques to aid the diagnosis. For this, it is necessary to understand molecular and protein mechanisms in the identification of diagnostic and predictive markers in the lesions. The Cyclin A1 protein, encoded by the CCNA1 gene, is an important cell cycle regulator, belonging to the MAPK/ERK signaling pathway directly involved with thyroid cancer. The aim of this study was to evaluate the CCNA1 gene and Cyclin A1 protein expression in papillary thyroid carcinoma, follicular thyroid carcinoma, and benign thyroid lesions, by real time quantitative PCR and immunohistochemistry analysis, respectively, to verify their roles as potential diagnostic and predictive markers to future applications in the clinical routine. Overexpression of CCNA1 gene was observed in the papillary carcinoma group compared to the normal group (P = 0.0023), benign lesions (P = 0.0011), colloid goiter (P = 0.0124), and follicular carcinoma (P = 0.0063). No differential expression was observed in the papillary primary tumor group from negative lymph nodes compared with the one from positive lymph nodes (P = 0.3818). Although an increased expression of Cyclin A1 was observed in the PTC group compared to the other one in the IHC analysis, no significant difference was observed (Fisher's exact Test). A Cyclin A1 overexpression was detected with weak to mid-moderate immunoreactivity in the benign group (k = 0.56), (score 1.5); mid-moderate to moderate in the goiter group (k = 0.58); weak in the FTC group (k = 0.33); and mid-moderate to moderate in the PTC group (k = 0.48). Due to the small sample size in the IHC analysis and to the fact that not all RNA is translated into protein, the diagnostic potential of Cyclin A1 could not be assessed. However, these findings highlight the potential of the CCNA1 gene as a diagnostic marker for papillary thyroid carcinoma.

Function, clinical application, and strategies of Pre-mRNA splicing in cancer

Pre-mRNA splicing is a fundamental process that plays a considerable role in generating protein diversity. Pre-mRNA splicing is also the key to the pathology of numerous diseases, especially cancers. In this review, we discuss how aberrant splicing isoforms precisely regulate three basic functional aspects in cancer: proliferation, metastasis and apoptosis. Importantly, clinical function of aberrant splicing isoforms is also discussed, in particular concerning drug resistance and radiosensitivity. Furthermore, this review discusses emerging strategies how to modulate pathologic aberrant splicing isoforms, which are attractive, novel therapeutic agents in cancer. Last we outline current and future directions of isoforms diagnostic methodologies reported so far in cancer. Thus, it is highlighting significance of aberrant splicing isoforms as markers for cancer and as targets for cancer therapy.

Clusterin inhibition mediates sensitivity to chemotherapy and radiotherapy in human cancer

Since its discovery in 1983, the protein clusterin (CLU) has been isolated from almost all human tissues and fluids and linked to the development of different physiopathological processes, including carcinogenesis and tumor progression. During the last few years, several studies have shown the cytoprotective role of secretory CLU in tumor cells, inhibiting their apoptosis and enhancing their resistance to conventional treatments including hormone depletion, chemotherapy, and radiotherapy. In an effort to determine the therapeutic potential that the inhibition of this protein could have on the development of new strategies for cancer treatment, numerous studies have been carried out in this field, with results, in most cases, satisfactory but sometimes contradictory. In this document, we summarize for the first time the current knowledge of the effects that CLU inhibition has on sensitizing tumor cells to conventional cancer treatments and discuss its importance in the development of new strategies against cancer.

Prognostic Role of Secretory Clusterin in Multiple Human Malignant Neoplasms: A Meta-Analysis of 26 Immunohistochemistry Studies

Secretory clusterin (sCLU) is a potential prognostic tumour biomarker, but results of different sCLU studies are inconsistent. We conducted this meta-analysis to evaluate the precise predictive value of sCLU. Qualified studies were identified by performing online searches in PubMed, EMBASE, and Web of Science. The selected articles were divided into three groups based on scoring method for clusterin detection. Pooled hazard ratios (HRs) with 95% confidence interval (CI) for patient survival and disease recurrence were calculated to determine the correlation between sCLU expression and cancer prognosis. Heterogeneity was assessed using I2 statistics, and specific heterogeneity in different groups was analysed. Elevated sCLU was significantly associated with recurrence-free survival in groups 1 and 3 (group 1: pooled HR = 1.35, 95% CI = 1.01 to 1.79; group 3: pooled HR = 1.80, 95% CI = 1.22 to 2.65). However, clusterin expression was not associated with overall survival in all three groups. Results showed that only the heterogeneity of group 2 was very strong (p = 0.013, I2 = 76.3%), in which the specimens were scored through sCLU staining intensity only. sCLU is a potential biomarker for tumour prognosis, and IHC methods can be more standardised if both intensity and staining proportion are considered.

Expression and Clinical Pathological Significance of miR-200a in Concurrent Cholangiocarcinoma Associated with Hepatolithiasis

Background

Approximately 2–10% of the patients with hepatolithiasis may develop cholangiocarcinoma (CCA). Despite recent advances in the treatment of cancers, the 5-year survival rate for CCA patients currently remains poor, primarily due to early local invasion and distant metastasis of the cancer. This study aimed to investigate miR-200a expression in combined hepatolithiasis and CCA as well as its correlation with the clinical features of CCA.

Material/Methods

miR-200a expression in combined hepatolithiasis and CCA was detected by real-time reverse transcription PCR (qRT-PCR). Its correlation with the clinicopathology of CCA was analyzed by t-tests. The effect of miR-200a on the proliferation CCA cells was determined by MTT assay. The effect of miR-200a on the invasive ability of CCA cells was assessed by Boyden chamber test.

Results

The expression level of MiR-200a in patients with combined hepatolithiasis and CCA was significantly decreased compared with patients with only hepatolithiasis (P<0.01). Furthermore, miR-200a expression in hepatic duct cancer RBE cells was substantially reduced compared with hepatolithiasis group (P<0.01). Correlation analysis showed that abnormal expression of miR-200a was only associated with the differentiation degree and metastasis of CCA. MiR-200a transfection significantly inhibited the proliferation and invasion of REB cells (P<0.01).

Conclusions

MiR-200a may suppress the proliferative and invasive ability of REB cells. The reduced miR-200a expression might be correlated with the development and progression of CCA.

Making many from few: IL-12p40 as a model for the combinatorial assembly of heterodimeric cytokines

How dendritic cells (DCs) gather information from the local milieu at a site of infection or injury and communicate this to influence adaptive immunity is not well understood. We and others have reported that soon after microbial encounter, DCs secrete the p40 subunit of IL-12, by itself, in a monomeric form. Based on recent data that this p40 monomer subsequently associates with p35 released from other cells to generate functional IL-12, we proposed that p40 can function as a DC-derived probe which samples the composition of the local milieu by looking for other binding partners. In this opinion, we discuss how such a sampling function might generate an elaborate combinatorial "code" of heterodimeric cytokines, capable of conveying location-specific information to cells downstream of DC activation, including NK and T cells.