Gene Expression Patterns Unveil New Insights in Papillary Thyroid Cancer

Diagnostic and Therapeutic Challenges in Parathyroid Cancers: 15 Years' Experience in a Tertiary Center and an Endocrine Surgery Referral Hospital

Background: Parathyroid cancers are rare endocrine malignancies that pose diagnostic and therapeutic challenges, particularly when discovered incidentally or in the presence of multiple endocrine disorders. This study aims to provide clinical, biochemical and pathological insights into these malignancies through a retrospective case series. Methods: We analyzed retrospectively, from a tertiary and an endocrine surgery referral center, 13 cases of parathyroid cancers, where 4 cases were associated with thyroid cancers, including demographic data, clinical presentation, biochemical markers, imaging, surgical interventions, histopathological findings and follow-up outcomes. Descriptive statistics were used to summarize patient characteristics. Results: The median age of the cohort was 64 (range: 40-81 years), with a female-to-male ratio of 8:5. More than half of the cases (61.53%) were diagnosed incidentally, with common biochemical findings including elevated parathyroid hormone (PTH) levels (median: 430 pg/mL) and hypercalcemia in 80% of the patients. All patients underwent surgery, with parathyroid resections with concomitant total thyroidectomy (62%) or lobectomy (23%) as the most common interventions. Histopathological analysis confirmed parathyroid carcinoma in all cases, with coexisting thyroid malignancies observed in 31%. An immunohistochemical profile performed in about half of the patients was in accordance with previously published data. Postoperative normalization of PTH levels was achieved in 77% of patients, and no recurrence or metastasis was observed in 85% of cases during follow-up. Conclusions: Despite the exceptional rarity of the disease, this case series highlights the importance of preoperative biochemical and imaging evaluation and the efficacy of surgical management. Long-term outcomes remain favorable with early diagnosis and diligent postoperative monitoring. Further research into molecular biomarkers and targeted therapies is warranted to improve the management of advanced or recurrent disease.

Pathogenesis and Management Strategies in Radioiodine-Refractory Differentiated Thyroid Cancer: From Molecular Mechanisms Toward Therapeutic Approaches: A Comprehensive Review

Thyroid cancer (TC) remains the most common cancer in endocrinology. Differentiated thyroid cancer (DTC), the most common type of TC, generally has a favorable outlook with conventional treatment, which typically includes surgery along with radioiodine (RAI) therapy and thyroid-stimulating hormone (TSH) suppression through thyroid hormone therapy. However, a small subset of patients (less than 5%) develop resistance to RAI. This resistance occurs due to the loss of Na/I symporter (NIS) activity, which is crucial for iodine absorption in thyroid cells. The decline in NIS activity appears to be due to gene modifications, reconfigurations with irregular stimulation of signaling pathways such as MAPK and PI3K/Akt pathways. These molecular changes lead to a diminished ability of DTC cells to concentrate iodine, which makes RAI therapy ineffective. As a consequence, patients with radioiodine-refractory DTC require alternative treatments. Therapy with tyrosine kinase inhibitors (TKIs) has emerged as the primary treatment option to inhibit proliferation and growth of RAIR-DTC, targeting the pathways responsible for tumor progression. In this article, we analyze molecular processes responsible for RAI resistance and explore both conventional and emerging therapeutic strategies for managing RAIR-DTC, aiming to improve patient outcomes.

A novel computational pathology approach for identifying gene signatures prognostic of disease-free survival for papillary thyroid carcinomas

INTRODUCTION

Papillary thyroid carcinoma (PTC) is the most prevalent form of thyroid cancer, with the classical and follicular variants representing most cases. Despite generally favorable prognoses, approximately 10% of patients experience recurrence post-surgery and radioactive iodine therapy. Attempts to stratify risk of recurrence have relied on gene expression-based prognostic and predictive signatures with a focus on mutations of well-known driver genes, while hallmarks of tumor morphology have been ignored.

OBJECTIVES

We introduce a new computational pathology approach to develop prognostic gene signatures for PTC that is informed by quantitative features of tumor and immune cell morphology.

METHODS

We quantified nuclear and immune-related features of tumor morphology to develop a pathomic signature, which was then used to inform an RNA-expression signature model provides a notable advancement in risk stratification compared to both standalone and pathology-informed gene-expression signatures.

RESULTS

There was a 17.8% improvement in the C-index (from 0.605 to 0.783) for 123 cPTCs and 15% (from 0.576 to 0.726) for 38 fvPTCs compared to the standalone gene-expression signature. Hazard ratios also improved for cPTCs from 0.89 (0.67,0.99) to 4.43 (3.65,6.68) and fvPTC from 0.98 (0.76,1.32) to 2.28 (1.87,3.64). We validated the image-based risk model on an independent cohort of 32 cPTCs with hazard ratio 1.8 (1.534,2.167).

VHL tumor suppressor as a novel potential candidate biomarker in papillary thyroid carcinoma

Papillary thyroid carcinoma (PTC) is the most common type of endocrine cancer, with an increasing incidence worldwide. The treatment of PTC is currently the subject of clinical controversy, making it critically important to identify molecular markers that would help improve the risk stratification of PTC patients and optimize the therapeutic approach. The VHL tumor suppressor gene has been implicated in tumorigenesis of various types of carcinoma and linked with their aggressive biological behavior. The role of VHL in the origin and development of PTC has only recently begun to be revealed. In this narrative review we attempt to summarize the existing knowledge that implicates VHL in PTC pathogenesis and to outline its potential significance as a candidate molecular biomarker for the grouping of PTC patients into high and low risk groups.

Identification of immune biomarkers associated with basement membranes in idiopathic pulmonary fibrosis and their pan-cancer analysis

Idiopathic pulmonary fibrosis (IPF) is a chronic progressive interstitial lung disease of unknown etiology, characterized by diffuse alveolitis and alveolar structural damage. Due to the short median survival time and poor prognosis of IPF, it is particularly urgent to find new IPF biomarkers. Previous studies have shown that basement membranes (BMs) are associated with the development of IPF and tumor metastasis. However, there is still a lack of research on BMs-related genes in IPF. Therefore, we investigated the expression level of BMs genes in IPF and control groups, and explored their potential as biomarkers for IPF diagnosis. In this study, the GSE32537 and GSE53845 datasets were used as training sets, while the GSE24206, GSE10667 and GSE101286 datasets were used as validation sets. In the training set, seven immune biomarkers related to BMs were selected by differential expression analysis, machine learning algorithm (LASSO, SVM-RFE, Randomforest) and ssGSEA analysis. Further ROC analysis confirmed that seven BMs-related genes played an important role in IPF. Finally, four immune-related Hub genes (COL14A1, COL17A1, ITGA10, MMP7) were screened out. Then we created a logistic regression model of immune-related hub genes (IHGs) and used a nomogram to predict IPF risk. The nomogram model was evaluated to have good reliability and validity, and ROC analysis showed that the AUC value of IHGs was 0.941 in the training set and 0.917 in the validation set. Pan-cancer analysis showed that IHGs were associated with prognosis, immune cell infiltration, TME, and drug sensitivity in 33 cancers, suggesting that IHGs may be potential targets for intervention in human diseases including IPF and cancer.

Surgical Outcomes of Thyroid Nodules Positive for Gene Expression Alterations Using ThyroSeq V3 Genomic Classifier

ThyroSeq V3 (TsV3) tests for various genetic alterations, including gene expression alterations (GEAs), to improve diagnostic accuracy and clinical decision-making for indeterminate thyroid nodules. This study aimed to clarify the clinico-pathological features and outcomes of GEA-positive thyroid nodules, which have not yet been well-described in the literature. A retrospective chart review was performed whereby patients were included if they underwent thyroid surgery between January 2018 and May 2022 at two McGill University teaching hospitals and their surgery was preceded by pre-operative molecular TsV3 testing. In total, 75 of the 328 patients with thyroid nodules (22.9%) who underwent molecular testing and surgery were GEA-positive. On surgical pathology, GEA-positive nodules showed a significantly higher malignancy rate compared to their GEA-negative counterparts (90.7% vs. 77.7%, respectively, p = 0.011). Among those that were malignant, 48.5% had at least one aggressive pathological feature, including histological subtype, extra-thyroidal extension, or lymph node metastasis. BRAF V600E mutation had a significantly greater association with aggressive malignant GEA-positive nodules compared to non-aggressive ones (p < 0.001). This study demonstrates that GEA may be an effective diagnostic and prognostic tool for thyroid nodule management. However, further investigation is needed to characterize the clinico-pathological features of GEA in isolation and in association with other gene alterations.

Prediction of EVT6-NTRK3-Dependent Papillary Thyroid Cancer Using Minor Expression Profile

Solid tumors resulting from oncogenic stimulation of neurotrophin receptors (TRK) by chimeric proteins are a group of rare tumors of various localization that respond to therapy with targeted drugs entrectinib and larotrectinib. The standard method for detecting chimeric TRK genes in tumor samples today is considered to be next generation sequencing with the determination of the prime structure of the chimeric transcripts. We hypothesized that expression of the chimeric tyrosine kinase proteins in tumors can determine the specific transcriptomic profile of tumor cells. We detected differentially expressed genes allowing distinguishing between TRK-dependent tumors papillary thyroid cancer (TC) from other molecular variants of tumors of this type. Using PCR with reverse transcription (RT-PCR), we identified 7 samples of papillary TC carrying a EVT6-NTRK3 rearrangement (7/215, 3.26%). Using machine learning and the data extracted from TCGA, we developed of a recognition function for predicting the presence of rearrangement in NTRK genes based on the expression of 10 key genes: AUTS2, DTNA, ERBB4, HDAC1, IGF1, KDR, NTRK1, PASK, PPP2R5B, and PRSS1. The recognition function was used to analyze the expression data of the above genes in 7 TRK-dependent and 10 TRK-independent thyroid tumors obtained by RT-PCR. On the test samples from TCGA, the sensitivity was 72.7%, the specificity - 99.6%. On our independent validation samples tested by RT-PCR, sensitivity was 100%, specificity - 70%. We proposed an mRNA profile of ten genes that can classify TC in relation to the presence of driver NTRK-chimeric TRK genes with acceptable sensitivity and specificity.

State of the Art in the Current Management and Future Directions of Targeted Therapy for Differentiated Thyroid Cancer

Two-thirds of differentiated thyroid cancer (DTC) patients with distant metastases would be classified as radioactive iodine-refractory (RAIR-DTC), evolving into a poor outcome. Recent advances underlying DTC molecular mechanisms have shifted the therapy focus from the standard approach to targeting specific genetic dysregulations. Lenvatinib and sorafenib are first-line, multitargeted tyrosine kinase inhibitors (TKIs) approved to treat advanced, progressive RAIR-DTC. However, other anti-angiogenic drugs, including single targeted TKIs, are currently being evaluated as alternative or salvage therapy after the failure of first-line TKIs. Combinatorial therapy of mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K) signalling cascade inhibitors has become a highly advocated strategy to improve the low efficiency of the single agent treatment. Recent studies pointed out targetable alternative pathways to overcome the resistance to MAPK and PI3K pathways’ inhibitors. Because radioiodine resistance originates in DTC loss of differentiation, redifferentiation therapies are currently being explored for efficacy. The present review will summarize the conventional management of DTC, the first-line and alternative TKIs in RAIR-DTC, and the approaches that seek to overcome the resistance to MAPK and PI3K pathways’ inhibitors. We also aim to emphasize the latest achievements in the research of redifferentiation therapy, immunotherapy, and agents targeting gene rearrangements in advanced DTC.

Atypia and Follicular Lesions of Undetermined Significance in Subsequent Biopsy Result: What Clinicians Need to Know

Atypia and follicular lesions of undetermined significance (AUS/FLUS) is the most controversial category of The Bethesda System. The risk of malignancy (ROM) in this group is estimated as 5–15%, however, the occurrence of two or more subsequent biopsy results with AUS/FLUS diagnosis makes these clinical situations more complex. We evaluated the ROM and prognostic value of aggressive ultrasound (US) features in 342 patients with thyroid nodules (TNs) with subsequent biopsy results of AUS/FLUS. We assessed US features and compared them with the final histopathological diagnosis. Overall, 121 (35.4%) individuals after first AUS/FLUS diagnosis underwent surgery and 221 (64.6%) patients had repeated biopsies. The ROM after first, second, and third biopsies with subsequent AUS/FLUS diagnosis were 7.4%, 18.5%, and 38.4% respectively. We demonstrated significantly higher rates of occurrence of aggressive US features in patients with malignancy (p < 0.0001). The age <55 years old was also a significant risk factor for TC (p = 0.044). Significant associations were found between aggressive US features and malignancy in patients after first diagnosis of AUS/FLUS (p < 0.05). The juxtaposition of US features with the number of biopsy repetitions of TN with consecutive AUS/FLUS diagnoses may simplify the decision-making process in surgical management. Two or three consecutive biopsy results with AUS/FLUS diagnosis increases the ROM.

An Assessment of InP/ZnS as Potential Anti-Cancer Therapy: Quantum Dot Treatment Increases Apoptosis in HeLa Cells

InP/ZnS quantum dots (QDs) are an emerging option in QD technologies for uses of fluorescent imaging as well as targeted drug and anticancer therapies based on their customizable properties. In this study we explored effects of InP/ZnS when treated with HeLa cervical cancer cells. We employed XTT viability assays, reactive oxygen species (ROS) analysis, and apoptosis analysis to better understand cytotoxicity extents at different concentrations of InP/ZnS. In addition, we compared the transcriptome profile from the QD-treated HeLa cells with that of untreated HeLa cells to identify changes to the transcriptome in response to the QD. RT-qPCR assay was performed to confirm the findings of transcriptome analysis, and the QD mode of action was illustrated. Our study determined both IC50 concentration of 69 µg/mL and MIC concentration of 167 µg/mL of InP/ZnS. It was observed via XTT assay that cell viability was decreased significantly at the MIC. Production of superoxide, measured by ROS assay with flow cytometry, was decreased, whereas levels of nitrogen radicals increased. Using analysis of apoptosis, we found that induced cell death in the QD-treated samples was shown to be significantly increased when compared to untreated cells. We conclude InP/ZnS QD to decrease cell viability by inducing stress via ROS levels, apoptosis induction, and alteration of transcriptome.

Thyroseq v3, Afirma GSC, and microRNA Panels Versus Previous Molecular Tests in the Preoperative Diagnosis of Indeterminate Thyroid Nodules: A Systematic Review and Meta-Analysis

BACKGROUND

Molecular tests are being used increasingly as an auxiliary diagnostic tool so as to avoid a diagnostic surgery approach for cytologically indeterminate thyroid nodules (ITNs). Previous test versions, Thyroseq v2 and Afirma Gene Expression Classifier (GEC), have proven shortcomings in malignancy detection performance.

OBJECTIVE

This study aimed to evaluate the diagnostic performance of the established Thyroseq v3, Afirma Gene Sequencing Classifier (GSC), and microRNA-based assays versus prior iterations in ITNs, in light of "rule-in" and "rule-out" concepts. It further analyzed the impact of noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) reclassification and Bethesda cytological subtypes on the performance of molecular tests.

METHODS

Pubmed, Scopus, and Web of Science were the databases used for the present research, a process that lasted until September 2020. A random-effects bivariate model was used to estimate the summary sensitivity, specificity, positive (PLR) and negative likelihood ratios (NLR), and area under the curve (AUC) for each panel. The conducted sensitivity analyses addressed different Bethesda categories and NIFTP thresholds.

RESULTS

A total of 40 eligible studies were included with 7,831 ITNs from 7,565 patients. Thyroseq v3 showed the best overall performance (AUC 0.95; 95% confidence interval: 0.93-0.97), followed by Afirma GSC (AUC 0.90; 0.87-0.92) and Thyroseq v2 (AUC 0.88; 0.85-0.90). In terms of "rule-out" abilities Thyroseq v3 (NLR 0.02; 95%CI: 0.0-2.69) surpassed Afirma GEC (NLR 0.18; 95%CI: 0.10-0.33). Thyroseq v2 (PLR 3.5; 95%CI: 2.2-5.5) and Thyroseq v3 (PLR 2.8; 95%CI: 1.2-6.3) achieved superior "rule-in" properties compared to Afirma GSC (PLR 1.9; 95%CI: 1.3-2.8). Evidence for Thyroseq v3 seems to have higher quality, notwithstanding the paucity of studies. Both Afirma GEC and Thyroseq v2 performance have been affected by NIFTP reclassification. ThyGenNEXT/ThyraMIR and RosettaGX show prominent preliminary results.

CONCLUSION

The newly emerged tests, Thyroseq v3 and Afirma GSC, designed for a "rule-in" purpose, have been proved to outperform in abilities to rule out malignancy, thus surpassing previous tests no longer available, Thyroseq 2 and Afirma GEC. However, Thyroseq v2 still ranks as the best rule-in molecular test.

SYSTEMATIC REVIEW REGISTRATION

http://www.crd.york.ac.uk/PROSPERO, identifier CRD42020212531.

Identification of Core Genes Involved in the Progression of Cervical Cancer Using an Integrative mRNA Analysis

In spite of being a preventable disease, cervical cancer (CC) remains at high incidence, and it has a significant mortality rate. Although hijacking of the host cellular pathway is fundamental for developing a better understanding of the human papillomavirus (HPV) pathogenesis, a major obstacle is identifying the central molecular targets involved in HPV-driven CC. The aim of this study is to investigate transcriptomic patterns of HPV-infected and normal tissues to identify novel prognostic markers. Analyses of functional enrichment and interaction networks reveal that altered genes are mainly involved in cell cycle, DNA damage, and regulated cell-to-cell signaling. Analysis of The Cancer Genome Atlas (TCGA) data has suggested that patients with unfavorable prognostics are more likely to have DNA repair defects attributed, in most cases, to the presence of HPV. However, further studies are needed to fully unravel the molecular mechanisms of such genes involved in CC.

The Prognostic Value of MicroRNAs in Thyroid Cancers-A Systematic Review and Meta-Analysis

Thyroid cancer (TC) includes various phenotypes, from indolent to highly aggressive cancer. The limitations of the current prognostication systems to predict the recurrence risk and the variability in expression of the genes involved in the thyroid carcinogenesis uncover the need for new prognostic biomarkers by taking into account potential epigenetic differences. We aimed to summarize the current knowledge regarding the prognostic impact of microRNAs (miRNAs) in TC. A literature search was conducted in PubMed, Embase, Scopus, and Web of Science databases. Both upregulated and downregulated miRNAs are significantly correlated with worse overall survival (hazard ratio (HR) = 5.94, 95% CI: 2.73-12.90, p < 0.001; HR = 0.51, 95% CI: 0.26-0.96, p = 0.048) disease/recurrence-free survival (HR = 1.58, 95% CI: 1.08-2.32, p = 0.003; HR = 0.37, 95%, CI: 0.24-0.60, p < 0.001). Sensitivity analysis revealed a significant association between the higher expression of miR-146b, miR-221, and miR-222 and the recurrence of papillary TC (OR = 9.11, 95% CI 3.00 to 27.52; p < 0.001; OR = 3.88, 95% CI 1.34 to 11.19, p < 0.001; OR = 6.56, 95% CI 2.75 to 15.64, p < 0.001). This research identified that miR-146b, miR-221, and miR-222 could serve as potential prognostic biomarkers in TC, particularly in PTC. Further studies are needed to strengthen these findings and sustain its clinical applicability.