Distinct molecular subtypes of papillary thyroid carcinoma and gene signature with diagnostic capability

Comprehensive Gene Expression Analysis in Papillary Thyroid Carcinoma Reveals a Transcriptional Profile Associated with Reduced Radioiodine Avidity

Papillary thyroid carcinoma (PTC) is the most common form of well-differentiated thyroid cancer (WDTC) and generally has a favorable prognosis. However, subsets of these tumors can metastasize, leading to aggressive disease progression and poorer clinical outcomes. Radioactive iodine (RAI) therapy is routinely given in the adjuvant setting following thyroidectomy and lymph node dissection for WDTC. Nevertheless, its therapeutic efficacy is limited to tumors with high iodine avidity. Early post-surgical classification of thyroid cancers as either iodine-avid or refractory is crucial for enabling more personalized and effective treatment strategies. In this study, we aimed to identify transcriptomic determinants associated with RAI refractoriness (RAI-R) to improve prognostication. We collected clinicopathologic data and conducted RNA-seq on 36 tissue samples (18 high-avidity and 18 low-avidity), each uniquely characterized by ex vivo iodine concentration measurements taken directly from surgical specimens. Whole-transcriptomic analysis identified 63 differentially expressed genes, with six (S100A4, CRTC2, ANO1, WWTR1, DEPTOR, MT1G) showing consistent deregulation. The expression of ANO1, an established iodine transporter at the apical membrane of the thyroid follicular cells, correlated significantly with iodine avidity (r = 0.54). Validation via RT-qPCR confirmed differential expression trends. Gene ontology and pathway enrichment analyses highlighted thyroid hormone synthesis, PI3K-AKT, and MAPK signaling pathways as key regulators of RAI avidity. A refined multivariate predictive model incorporating ANO1 mRNA expression, histological subtypes, and sample type demonstrated strong predictive performance (adjusted R2 = 0.55). These findings suggest ANO1 as a promising biomarker for predicting iodine avidity in thyroid cancer.

CALML6 as a potential diagnostic marker for thyroid cancer promotes thyroid cancer cell proliferation via modulating the immune microenvironment

PURPOSE

CALML6 is an inflammation-related gene, and its expression may be associated with cancer. Here we evaluated the role of CALML6 expression in papillary thyroid carcinoma (PTC).

METHODS

We utilized databases such as The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression Project (GTEx) and UALCAN to evaluate the relationship between CALML6 expression and clinicopathological features in thyroid cancer. Immunohistochemical assays were used to observe CALML6 expression in thyroid cancer tissues. The role of CALML6 in PTC cells was investigated using RNA interference.

RESULTS

We found CALML6 expression was lower than normal and associated with extrathyroidal extension, lymph node metastasis, pathological T stage, tall cell PTC and the expressions of immune checkpoint genes CD274 and PDCD1LG2 in THCA. Additionally, Immunohistochemical staining showed that CALML6 expression was significantly upregulated in thyroid cancer tissues. RNAi analysis showed that CALML6 knockdown significantly reduced cell growth and blocked the cell cycle of PTC cells.

CONCLUSIONS

Our results suggest that CALML6 may be a novel diagnostic marker for PTC that is closely associated with the invasive and tall cell subtypes, and it may be a potential target for immunotherapy.

Analysis of BRAF Gene Mutation in Hashimoto's Thyroiditis With Multifocal Papillary Thyroid Carcinoma

BACKGROUND

Thyroid cancer (TC) is a highly prevalent malignant tumor of the head and neck. Papillary thyroid carcinoma (PTC) is the primary pathological type of TC, accounting for more than 80% of all TCs. BRAF mutations are closely associated with PTC. However, the relationship among HT, PTC, and BRAF mutations has not yet been clarified. We aimed to investigate the BRAF mutation in Hashimoto's thyroiditis (HT) with PTC.

METHODS

A total of 72 patients with multifocal PTC were included and grouped based on surgical pathology examination. Group A (n = 32) had pure multifocal PTC and Group B (n = 40) had HT with multifocal PTC. Various features were compared: BRAF mutation, multifactorial analysis of BRAF mutations, pathological features in patients with HT and multifocal PTC, and multifactorial analysis of factors affecting HT with multifocal PTC.

RESULTS

Significant differences were seen in thyroid peroxidase antibody levels, central lymph node metastasis, extra-thyroidal invasion, main and non-main lesion diameters, and BRAF mutation positivity (P < 0.05). Patients with the BRAF mutation had significantly higher rates of extra-thyroidal invasion and lymph node metastasis than those without the BRAF mutation (P < 0.05). Logistic regression analysis showed that BRAF mutation and main lesion nodule diameter were independent risk factors affecting extra-thyroidal invasion and central lymph node metastasis in patients with HT and multifocal PTC (P < 0.05).

DISCUSSION

BRAF mutations were more prevalent and closely associated with extra-thyroidal invasion and central lymph node metastasis in patients with HT and multifocal PTC.

Modulation of Intestinal Flora: a Novel Immunotherapeutic Approach for Enhancing Thyroid Cancer Treatment

Over the past 3 years, there has been a growing interest in clinical research regarding the potential involvement of intestinal flora in thyroid cancer (TC). This review delves into the intricate connection between intestinal flora and TC, focusing on the particular intestinal flora that is directly linked to the disease and identifying which may be able to predict potential microbial markers of TC. In order to shed light on the inflammatory pathways connected to the onset of TC, we investigated the impact of intestinal flora on immune modulation and the connection between chronic inflammation when investigating the role of intestinal flora in the pathogenesis of TC. Furthermore, the potential role of intestinal flora metabolites in the regulation of thyroid function was clarified by exploring the effects of short-chain fatty acids and lipopolysaccharide on thyroid hormone synthesis and metabolism. Based on these findings, we further explore the effects of probiotics, prebiotics, postbiotics, vitamins, and trace elements.

Integrating multiomics analysis and machine learning to refine the molecular subtyping and prognostic analysis of stomach adenocarcinoma

Stomach adenocarcinoma (STAD) is a common malignancy with high heterogeneity and a lack of highly precise treatment options. We downloaded the multiomics data of STAD patients in The Cancer Genome Atlas (TCGA)-STAD cohort, which included mRNA, microRNA, long non-coding RNA, somatic mutation, and DNA methylation data, from the sxdyc website. We synthesized the multiomics data of patients with STAD using 10 clustering methods, construct a consensus machine learning-driven signature (CMLS)-related prognostic models by combining 10 machine learning methods, and evaluated the prognosis models using the C-index. The prognostic relationship between CMLS and STAD was assessed using Kaplan-Meier curves, and the independent prognostic value of CMLS was determined by univariate and multivariate regression analyses. we also evaluated the immune characteristics, immunotherapy response, and drug sensitivity of different CMLS groups. The results of the multiomics analysis classified STAD into three subtypes, with CS1 resulting in the best survival outcome. In total, 10 hub genes (CES3, AHCYL2, APOD, EFEMP1, CYP1B1, ASPN, CPE, CLIP3, MAP1B, and DKK1) were screened and constructed the CMLS was significantly correlated with prognosis in patients with STAD and was an independent prognostic factor for patients with STAD. Using the CMLS risk score, all patients were divided into a high CMLS group and a low CMLS group. Patients in the low-CMLS group had better survival, more enriched immune cells, and higher tumor mutation load scores, suggesting better immunotherapy responsiveness and a possible "hot tumor" phenotype. Patients in the high-CMLS group had a significantly poorer prognosis and were less sensitive to immunotherapy but were likely to benefit more from chemotherapy and targeted therapy. In this study, 10 clustering methods and 10 machine learning methods were combined to analyze the multiomics of STAD, classify STAD into three subtypes, and constructed CMLS-related prognostic model features, which are important for accurate management and effective treatment of STAD.

TM4SF4 is a diagnostic biomarker accelerating progression of papillary thyroid cancer via AKT pathway

The incidence of papillary thyroid cancer (PTC) has been steadily rising, though the underlying mechanism remains unclear. This study aims to elucidate the biological role of TM4SF4 in the PTC progression. Our differential expression analysis indicated that TM4SF4 was significantly upregulated in PTC, which was corroborated in both our local cohort and the data from Human Protein Atlas. Additionally, clinical characteristics analysis and receiver operating characteristic curves (ROC) demonstrated that TM4SF4 served as a significant diagnostic marker for PTC. Correlation and enrichment analysis of TM4SF4-related partners suggested that it was involved in cell junction and cohesion processes. Furthermore, immune infiltration analysis revealed a positive correlation between TM4SF4 expression and the immune activation in PTC. Importantly, in vitro experiments demonstrated that TM4SF4 downregulation suppressed the proliferation and metastasis of PTC cell lines while inducing apoptosis. We further discovered that the AKT activator SC79 was able to reverse the malignant behaviors suppression caused by TM4SF4 knockdown, suggesting that TM4SF4 may promote PTC progression via the AKT pathway. In conclusion, our study highlights the oncogenic role of TM4SF4 in PTC and identifies it as a novel biomarker for diagnosis and treatment.

KRT80 in hepatocellular carcinoma plays oncogenic role via epithelial-mesenchymal transition and PI3K/AKT pathway

Hepatocellular carcinoma (HCC), a globally prevalent form of cancer, is featured by aggressive growth and early metastasis. Elucidating the underlying mechanism and identifying the effective therapy are critical for advanced HCC patients. In the study, we detect that KRT80 was upregulated in HCC samples. HCC patients with higher KRT80 are associated with worse overall survival after surgery. Gain-of and loss-of function studies show that KRT80 enhanced HCC cells proliferation, migration, invasion, and angiogenesis, whereas its silencing abolishes the effects in vivo and in vitro. Mechanistic investigation shows that KRT80 may function as an independent prognostic risk factor and act as an oncogene by influencing EMT and modulating the PI3K/AKT signaling pathway. Together, these findings suggest that KRT80 may be a potential oncogene and a good indicator in predicting prognosis. Targeting KRT80 can offer new insights into the prevention and treatment of HCC.

A computational approach to assessing the prognostic implications of BRAF and RAS mutations in patients with papillary thyroid carcinoma

Papillary thyroid carcinoma (PTC) is the most common thyroid cancer, posing a growing clinical challenge. PTC exhibits two age-related peaks, with established risk factors including family history and radiation exposure. Managing even low-risk, localized PTC cases remain complex, with growing interest in active surveillance as an alternative to immediate surgery. This study employed single-cell RNA sequencing (scRNA-Seq) to explore the predictive value of BRAF and RAS mutations in PTC, shedding light on their impact on disease progression and outcomes. The analyses emphasized the significance of BRAF and RAS mutations in tumor advancement, particularly the unique BRAF V600E mutation associated with aggressive features. The methodology involved scRNA-Seq analysis of PTC and normal samples, unveiling distinct cell clusters and indicating upregulated BRAF and RAS genes. Pathway enrichment analysis highlighted altered biological processes and immune-related pathways in PTC. The study consolidated previous research showing the prevalence of BRAF and RAS mutations in PTC, subtypes with distinct molecular profiles, and the impact of TERT promoter mutations on disease severity. In summary, this study unveils the complex interplay of genetic mutations and the cellular microenvironment in PTC through scRNA-Seq. The upregulated BRAF and RAS genes suggest their roles as PTC drivers, and pathway enrichment reveals alterations in immune-related processes. This synthesis of prior research enhances our understanding of PTC's molecular foundations, informing better prognosis and personalized treatment approaches. These insights advance the landscape of PTC management and provide directions for further research.

Construction and validation of a nomogram for predicting cervical lymph node metastasis in tall cell variant of papillary thyroid carcinoma

OBJECTIVE

To analyze the risk factors associated with the occurrence of cervical lymph node metastasis (LNM) in patients with tall cell variant of papillary thyroid carcinoma (TCV-PTC) and to establish a nomogram.

METHODS

Clinical data of 727 patients with TCV-PTC from SEER database were obtained, and they were randomly divided into the training group (n = 508) and validation group (n = 219). The clinicopathological characteristics were analyzed by logistic regression, including age, marital status, race, gender, tumor size(cm), T stage, M stage, bilaterality, capsular invasion, extrathyroidal extension (ETE), vascular invasion and multifocality. The C-index, calibration curves, and DCA were utilized to validate the model from the differentiation and calibration of the nomogram, respectively.

RESULTS

Tumor size, extrathyroidal extension, and multifocality were independent risk factors for the development of LNM in patients with TCV-PTC (P < 0.05). In the training and validation groups, the C-index of internal validation of the nomogram were 0.727 (95% CI: 0.571-0.785) and 0.712 (95%CI: 0.700-0.714). The calibration curves indicated that the model was in good agreement, and the DCA indicated that the nomogram model had good clinical utility.

CONCLUSION

Tumor size, extrathyroidal extension, and multifocality are independent risk factors for developing LNM in TCV-PTC. The nomogram model can predict the risk of developing LNM in TCV-PTC patients and provide clinical guidance.

Estrogen enhances the proliferation, migration, and invasion of papillary thyroid carcinoma via the ERα/KRT19 signaling axis

BACKGROUND

Estrogen is thought to be the reason for the higher prevalence of papillary thyroid carcinoma (PTC) in fertile women; however, more study is required to completely comprehend how estrogen affects PTC development at the cellular level. Therefore, we combined Oxford Nanopore Technologies (ONT) sequencing to explore molecular markers of PTC and to investigate the molecular mechanisms by which estrogen promotes PTC development.

METHODS

The expression levels of ESR1 (ERα) and KRT19 in normal thyroid tissues and cancer tissues as well as in different cancer stages, races, genders, age groups, histological subtypes and nodular metastasis status of the TCGA database were analyzed online by Ualcan; the relationship between ESR1, KRT19 and the survival of THCA patients was analyzed. A PTC xenograft tumor model was established. An ERα specific inhibitor (MPP) was administered and an EDU cell proliferation assay was used to verify the effect of estrogen on PTC proliferation. KRT19 was knocked down in KTC-1 cells, and the proliferation, migration, and invasion abilities of PTC cells were determined using CCK-8, immunofluorescence labeling, Western blot for EMT-related proteins, scratch assay, and Transwell assay. The role of ERα in relation to KRT19 was investigated by Western blot and immunofluorescence. The effects of ERα/KRT19 signaling axis on the proliferation, migration and invasion ability of PTC cells were evaluated using EDU cell proliferation assay and Transwell. Using ONT sequencing, 15 pairs of PTC tissue and paracancer tissue samples were collected. A PPI network was constructed to validate the differential expression of KRT19 in combination with biosignature analysis, and the protein interaction between KRT19 and ESR1 was verified using STRING.

RESULTS

Ualcan showed that the expression of ESR1 and KRT19 was higher in THCA tissues than in normal thyroid tissues. E2 activation of ERα promoted the growth of PTC cells and tissues. si-KRT19 inhibited the proliferation, migration and invasion of PTC cells. KRT19 together with ERα formed the ERα/KRT19 signaling axis. E2 activation of the ERα/KRT19 signaling axis promoted the proliferation, migration, and invasion of PTC cells. ONT sequencing and STRING website verified that KRT19 is significantly differentially expressed in PTC and that ESR1 and KRT19 have protein interactions and are related to the estrogen signaling pathway.

CONCLUSIONS

Using public databases, RNA sequencing, and bioinformatics, we discovered that E2 stimulates the ERα/KRT19 signaling axis to stimulate PTC proliferation, migration, and invasion.

Expression of CLDN1 and EGFR in PTC

Papillary thyroid carcinoma (PTC) involves complex genetic mechanisms, notably involving CLDN1 and EGFR. This study investigates the expression and variations of these genes and their effects on tumor behavior and patient outcomes. Meta-analysis of CLDN1 and EGFR expression in TCGA-PTC patients and GEO datasets was conducted. cBioPortal was used for clinical analysis. GSEA, GO, KEGG, Hallmark pathways, and cibersort analysis were applied. Cell proliferation, migration, invasion, and apoptosis were assessed in vitro. Co-culturing with CD8+ T cells, MTT assay, ELISA, subcutaneous tumor models, and immunohistochemistry were performed. TGF-β pathway-related proteins were analyzed via Western blot. CLDN1 and EGFR were overexpressed in PTC tumors, correlating with higher-risk patients and reduced CD8+ T cell infiltration. Silencing these genes inhibited tumor cell functions and enhanced CD8+ T cell activity, both in vitro and in vivo. CLDN1 and EGFR are crucial in PTC, linked to tumor invasiveness, EMT, and immune suppression, presenting them as potential therapeutic targets.

The evolving process of ferroptosis in thyroid cancer: Novel mechanisms and opportunities

Thyroid cancer (TC) is a prevalent endocrine malignancy, with a significant increase in incidence worldwide. Ferroptosis is a novel form of programmed cell death, primarily caused by iron overload and reactive oxygen species (ROS)-dependent accumulation of lipid peroxides. The main manifestations of cellular ferroptosis are rupture of the outer membrane, crumpling of the mitochondria and shrinkage or disappearance of the mitochondrial cristae, thus leading to cell death. Ferroptosis is an important phenomenon in tumour progression, with crosstalk with tumour-associated signalling pathways profoundly affecting tumour progression, immune effects and treatment outcomes. The functions and mechanisms of ferroptosis in TC have also attracted increasing attention, mainly in terms of influencing tumour proliferation, invasion, migration, immune response, therapeutic susceptibility and genetic susceptibility. However, at present, the tumour biology of the morphological, biological and mechanism pathways of ferroptosis is much less deep in TC than in other malignancies. Hence, in this review, we highlighted the emerging role of ferroptosis in TC progression, including the novel mechanisms and potential opportunities for diagnosis and treatment, as well as discussed the limitations and prospects. Ferroptosis-based diagnostic and therapeutic strategies can potentially provide complementary management of TCs.

Value of Multimodal Ultrasound Combined with BRAF Gene in Evaluating Cervical Lymph Node Metastasis of Papillary Thyroid Microcarcinoma

OBJECTIVE

The aim of the work described here was to explore the predictive value of multimodal ultrasound combined with the BRAF gene in cervical lymph node metastasis (CLNM) of papillary thyroid microcarcinoma (PTMC).

METHODS

One hundred six patients (114 lesions) with PTMC confirmed by surgery and pathology at Yantai Yuhuangding Hospital from July 2021 to August 2022 were analyzed retrospectively. Routine ultrasound, contrast-enhanced ultrasound, shear wave elastography examination and BRAF V600E gene detection were performed before surgery. Patients were divided into two groups on the basis of post-operative pathology: non-metastasis group and metastasis group. Univariate and multivariate analyses were used to analyze the risk factors of cervical lymph node metastasis in PTMC.

RESULTS

Univariate analysis revealed that there were significant differences in gender, high echo in lesions, enhancement level, peak intensity (PI) and average modulus of elasticity (Eavg) between the two groups (p < 0.05), but there was no significant difference in BRAF gene mutation (p = 0.855). Multivariate analysis revealed that male gender, microcalcification and hyper- or iso-enhancing parametric increased the risk of CLNM in PTMC (p < 0.05), and that sensitivity (92.3%) and accuracy (73.9%) were higher for combined diagnosis than for single diagnosis; the differences were statistically significant (p < 0.05).

CONCLUSION

Male gender, microcalcification and hyper- or iso-enhancing parametrics of CEUS are independent risk factors for CLNM in PTMC patients. Combined diagnosis is more effective.

TLE4 downregulation identified by WGCNA and machine learning algorithm promotes papillary thyroid carcinoma progression via activating JAK/STAT pathway

Background: Papillary Thyroid Carcinoma (PTC), a common type of thyroid cancer, has a pathogenesis that is not fully understood. This study utilizes a range of public databases, sophisticated bioinformatics tools, and empirical approaches to explore the key genetic components and pathways implicated in PTC, particularly concentrating on the Transducin-Like Enhancer of Split 4 (TLE4) gene. Methods: Public databases such as TCGA and GEO were utilized to conduct differential gene expression analysis in PTC. Hub genes were identified using Weighted Gene Co-expression Network Analysis (WGCNA), and machine learning techniques, including Random Forest, LASSO regression, and SVM-RFE, were employed for biomarker identification. The clinical impact of the TLE4 gene was assessed in terms of diagnostic accuracy, prognostic value, and its functional enrichment analysis in PTC. Additionally, the study focused on understanding the role of TLE4 in the dynamics of immune cell infiltration, gene function enhancement, and behaviors of PTC cells like growth, migration, and invasion. To complement these analyses, in vivo studies were performed using a xenograft mouse model. Results: 244 genes with significant differential expression across various databases were identified. WGCNA indicated a strong link between specific gene modules and PTC. Machine learning analysis brought the TLE4 gene into focus as a key biomarker. Bioinformatics studies verified that TLE4 expression is lower in PTC, linking it to immune cell infiltration and the JAK-STAT signaling pathways. Experimental data revealed that decreased TLE4 expression in PTC cell lines leads to enhanced cell growth, migration, invasion, and activates the JAK/STAT pathway. In contrast, TLE4 overexpression in these cells inhibited tumor growth and metastasis. Conclusions: This study sheds light on TLE4's crucial role in PTC pathogenesis, positioning it as a potential biomarker and target for therapy. The integration of multi-omics data and advanced analytical methods provides a robust framework for understanding PTC at a molecular level, potentially guiding personalized treatment strategies.

Clinical value of ultrasound parameters PI, TTP, and MTT in assessing cervical lymph node metastasis of papillary thyroid carcinoma

OBJECTIVE

To determine the clinical value of ultrasound in assessing cervical lymph node metastasis (CLNM) in papillary thyroid carcinoma (PTC).

METHODS

The medical records of 179 PTC patients treated in Shandong Provincial Qianfoshan Hospital between March 2016 and March 2019 were collected. The patients were assigned to a transfer group (54 cases) and a non-transfer group (125 cases) according to their pathologic results. The ultrasound parameters (peak intensity (PI), time to peak (TTP), and mean transit time (MTT)) of the two groups were compared. Then, multivariate logistic regression was used to analysis the results, and receiver operating characteristic (ROC) curves were plotted to evaluate the value of risk factors in predicting CLNM.

RESULTS

The transfer group showed notably lower PI, TTP and MTT than the non-transfer group (P<0.001), and focus diameter, microcalcification, multiple foci, PI, TTP, and MTT were identified as independent risk factors for LNM in patients (P<0.05). According to the ROC curve, the areas under the curves (AUCs) of microcalcification, multiple foci, and PI were all smaller than 0.7; the AUCs of focus diameter and MTT were smaller than 0.8, and the AUC of TTP was 0.855.

CONCLUSION

PI, TTP, and MTT all decrease in PTC patients with CLNM, and TTP has a strong predictor for CLNM in them, with an AUC of 0.855.

Spatial transcriptomics reveals prognosis-associated cellular heterogeneity in the papillary thyroid carcinoma microenvironment

BACKGROUND

Papillary thyroid carcinoma (PTC) is the most common malignant endocrine tumour, and its incidence and prevalence are increasing considerably. Cellular heterogeneity in the tumour microenvironment is important for PTC prognosis. Spatial transcriptomics is a powerful technique for cellular heterogeneity study.

METHODS

In conjunction with a clinical pathologist identification method, spatial transcriptomics was employed to characterise the spatial location and RNA profiles of PTC-associated cells within the tissue sections. The spatial RNA-clinical signature genes for each cell type were extracted and applied to outlining the distribution regions of specific cells on the entire section. The cellular heterogeneity of each cell type was further revealed by ContourPlot analysis, monocle analysis, trajectory analysis, ligand-receptor analysis and Gene Ontology enrichment analysis.

RESULTS

The spatial distribution region of tumour cells, typical and atypical follicular cells (FCs and AFCs) and immune cells were accurately and comprehensively identified in all five PTC tissue sections. AFCs were identified as a transitional state between FCs and tumour cells, exhibiting a higher resemblance to the latter. Three tumour foci were shared among all patients out of the 13 observed. Notably, tumour foci No. 2 displayed elevated expression levels of genes associated with lower relapse-free survival in PTC patients. We discovered key ligand-receptor interactions, including LAMB3-ITGA2, FN1-ITGA3 and FN1-SDC4, involved in the transition of PTC cells from FCs to AFCs and eventually to tumour cells. High expression of these patterns correlated with reduced relapse-free survival. In the tumour immune microenvironment, reduced interaction between myeloid-derived TGFB1 and TGFBR1 in tumour focus No. 2 contributed to tumourigenesis and increased heterogeneity. The spatial RNA-clinical analysis method developed here revealed prognosis-associated cellular heterogeneity in the PTC microenvironment.

CONCLUSIONS

The occurrence of tumour foci No. 2 and three enhanced ligand-receptor interactions in the AFC area/tumour foci reduced the relapse-free survival of PTC patients, potentially leading to improved prognostic strategies and targeted therapies for PTC patients.

Insight of novel biomarkers for papillary thyroid carcinoma through multiomics

Introduction

The overdiagnosing of papillary thyroid carcinoma (PTC) in China necessitates the development of an evidence-based diagnosis and prognosis strategy in line with precision medicine. A landscape of PTC in Chinese cohorts is needed to provide comprehensiveness.

Methods

6 paired PTC samples were employed for whole-exome sequencing, RNA sequencing, and data-dependent acquisition mass spectrum analysis. Weighted gene co-expression network analysis and protein-protein interactions networks were used to screen for hub genes. Moreover, we verified the hub genes' diagnostic and prognostic potential using online databases. Logistic regression was employed to construct a diagnostic model, and we evaluated its efficacy and specificity based on TCGA-THCA and GEO datasets.

Results

The basic multiomics landscape of PTC among local patients were drawn. The similarities and differences were compared between the Chinese cohort and TCGA-THCA cohorts, including the identification of PNPLA5 as a driver gene in addition to BRAF mutation. Besides, we found 572 differentially expressed genes and 79 differentially expressed proteins. Through integrative analysis, we identified 17 hub genes for prognosis and diagnosis of PTC. Four of these genes, ABR, AHNAK2, GPX1, and TPO, were used to construct a diagnostic model with high accuracy, explicitly targeting PTC (AUC=0.969/0.959 in training/test sets).

Discussion

Multiomics analysis of the Chinese cohort demonstrated significant distinctions compared to TCGA-THCA cohorts, highlighting the unique genetic characteristics of Chinese individuals with PTC. The novel biomarkers, holding potential for diagnosis and prognosis of PTC, were identified. Furthermore, these biomarkers provide a valuable tool for precise medicine, especially for immunotherapeutic or nanomedicine based cancer therapy.

Performance of multigene testing in cytologically indeterminate thyroid nodules and molecular risk stratification

Objective

Thyroid cancer is the third most prevalent cancer among females. Genetic testing based on next-generation sequencing may provide an auxiliary diagnosis to reduce cytologically diagnostic uncertainty. However, commercial multigene tests are not widely available and are not well-tested in the Chinese population.

Methods

In this study, we designed a multigene testing panel and evaluated its performance in 529 cytologically indeterminate thyroid nodules (Bethesda III, IV and V). The molecular data of the DNA mutations and RNA fusions of fine needle aspiration samples were reviewed in conjunction with a clinical diagnosis, pathological reports, and definitive surgery for retrospective analysis. Then, the molecular risk stratification was investigated for its accuracy in malignant risk prediction.

Results

The overall combined consistency revealed substantial agreement (Kappa = 0.726) with the sensitivity, specificity, positive predictive value, and negative predictive values of 97.80%, 82.14%, 98.99%, and 67.65%, respectively. The most common aberration was BRAFV600E (82.59%), followed by NRAS mutants (4.07%), RET fusions (3.70%), and KRAS mutants (3.15%). Two cases (0.44%) were categorized into a high-risk group, 426 cases (94.67%) were categorized into a BRAF-like group with totally histopathologic papillary patterned tumors, and 22 cases (4.89%) were categorized into a RAS-like group with 14 papillary and eight follicular patterned tumors when the cohort concurrent aberrations were excluded. Potentially aggressive features may be related to concurrent molecular alterations of BRAFV600E with TERTQ302R, and AKT1L52R, NRASG12C, NRASQ61R, and CCDC6-RET fusions.

Conclusions

This study provided a multigene panel for identifying benign nodules from cytologically indeterminate thyroid nodules to avoid unnecessary surgery. We provide further evidence for using molecular risk stratification as a promising predictor of disease outcomes. The results of this study may be limited by the extremely high prevalence of cancer in the cohort for clinical reference.

The association of hypoxia-inducible factor-1α and hypoxia-inducible factor-2α protein expression with clinicopathological characteristics in papillary thyroid carcinoma: A meta-analysis

OBJECTIVE

To investigate the correlation of hypoxia-inducible factor-1α (HIF-1α) and hypoxia-inducible factor-2α (HIF-2α) protein expression with clinicopathologic characteristics in patients with papillary thyroid carcinoma (PTC) through a meta-analysis.

METHODS

PubMed, Embase, Web of Science, Cochrane, CNKI, Wanfang, and VIP databases were searched from the establishment of the database to February 2023. The New castle-Ottawa Scale was used to evaluate the quality of the literature. Rev Man 5.3 and Stata14.0 were used to conduct a meta-analysis of the included studies.

RESULTS

Twenty-eight articles with 2346 samples were included in the Meta-analysis. Compared with normal thyroid tissues, HIF-1α and HIF-2α proteins were highly expressed in PTC tumor tissues. High expression of HIF-1α protein was associated with tumor size (odds ratio [OR] = 4.50, 95% confidence interval [CI]: 2.88-7.04, P < .00001), lymph node metastasis (OR = 4.76, 95% CI: 3.78-5.99, P < .00001), TNM stage (OR = 3.67, 95% CI: 2.68-5.03, P < .00001), capsular invasion (OR = 2.30, 95% CI: 1.43-3.71, P = .0006 < .05), and extrathyroidal extension (OR = 10.96, 95% CI: 4.80-25.02, P < .00001). High expression of HIF-2α protein was associated with lymph node metastasis (OR = 4.18, 95% CI: 2.63-6.65, P < .00001), TNM stage (OR = 2.56, 95% CI: 1.36-4.82, P = .004 < .05), and capsular invasion (OR = 3.84, 95% CI: 1.66-8.88, P = .002 < .05). In addition, we concluded for the first time that there was a statistically significant difference in the expression of HIF-1α and HIF-2α in PTC patients (OR = 2.36, 95% CI: 1.26-4.42, P = .007 < .05).

CONCLUSIONS

The high expression of HIF-1α and HIF-2α proteins is closely related to some clinicopathological parameters of PTC, and can provide potential biological indicators for the diagnosis and prognosis of PTC.

Multi-omics profiling of papillary thyroid microcarcinoma reveals different somatic mutations and a unique transcriptomic signature

BACKGROUND

Papillary thyroid microcarcinoma (PTMC) incidence has significantly increased, and some cases still exhibit invasive traits. The entire molecular landscape of PTMC, which can offer hints for the etiology of cancer, is currently absent.

METHODS

We compared our findings with those for PTMC in the TCGA by analyzing the largest study at the current stage of whole exome sequencing and RNA-sequencing data from 64 patients with PTMC. Then, we systematically demonstrated the differences between the two PTMC subtypes based on multi-omics analyses. Additionally, we created a molecular prediction model for the PTMC subtypes and validated them among TCGA patients for individualized integrative assessment.

RESULTS

In addition to the presence of BRAF mutations and RET fusions in the TCGA cohort, we also discovered a new molecular signature named PTMC-inflammatory that implies a potential response to immune intervention, which is enriched with AFP mutations, IGH@-ext fusions, elevated immune-related genes, positive peroxidase antibody, and positive thyroglobulin antibody. Additionally, a molecular prediction model for the PTMC-inflammatory patients was created and validated among TCGA patients, while the prognosis for these patients is poor.

CONCLUSIONS

Our findings comprehensively define the clinical and molecular features of PTMC and may inspire new therapeutic hypotheses.

STRA6 regulates tumor immune microenvironment and is a prognostic marker in BRAF-mutant papillary thyroid carcinoma

BACKGROUND

BRAF mutation is one of the most common genetic alterations contributing to the initiation and progression of papillary thyroid carcinoma (PTC). However, the prognostic value of BRAF mutation for PTC is limited. Novel markers are needed to identify BRAF-mutant patients with poor prognosis.

METHODS

Transcriptional expression data were downloaded from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Pathway enrichment was performed by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and gene set enrichment analysis (GSEA). Protein-protein interaction networks were predicted by the GeneMANIA. The correlation between STRA6 expression and immune infiltration was analyzed by tumor immune estimation resource (TIMER) and tumor-immune system interaction database (TISIDB). Immunohistochemistry was used to detect the STRA6 protein expression level of PTC. Infiltration of regulatory T cells (Tregs) and CD8+ T cells in tumor samples were analyzed by fluorescent multiplex immunohistochemistry.

RESULTS

In BRAF-mutant PTC, STRA6 was extremely upregulated and predicted unfavorable survival, which was an independent risk factor for increased mortality risk. Bioinformatic analyses indicated that STRA6 might activate the MAPK pathway synergistically with BRAF^V600E. The expression of STRA6 was associated with immune infiltrates and T cell exhaustion. Fluorescent multiplex immunohistochemistry showed that STRA6 increased Tregs abundance and decreased CD8+ T cells infiltration in PTC. Moreover, STRA6 promoted epithelial-mesenchymal transition via increased cancer-associated fibroblasts infiltration.

CONCLUSIONS

Our study demonstrates STRA6 may serve as a prognostic marker for BRAF-mutated PTC, which may drive thyroid carcinogenesis via activation of oncogenic pathway and regulation of tumor immunosuppressive microenvironment.