GPCR-mediated PI3K pathway mutations in pediatric and adult thyroid cancer

Prevalent genetic alterations in pediatric thyroid carcinoma: Insights from an Argentinean study

Thyroid cancer is the primary endocrine malignancy, exhibiting distinct genomic drivers. The frequency of genetic alterations varies between adult and pediatric groups and across geographic regions and ethnicities. Molecular markers may serve as prognostic tools and/or specific treatment-selection tools in papillary thyroid carcinoma (PTC) in children. We sought to characterize molecular alterations in pediatric PTC from Argentina and test a future laboratory algorithm for molecular diagnosis and stratification. Immunohistochemistry, fluorescence in situ hybridization, and Sanger sequencing were performed on 57 pediatric PTC samples. This study assesses multiple genetic alterations, including fusions in RET, ALK, MET, BRAF, and NTRK genes, as well as the BRAF V600E single nucleotide variant. Fusions in known oncogenes were observed in 29.8% of cases (6 in RET, 5 in ALK, 4 in NTRK3, 1 in BRAF, and 1 in MET). The BRAF V600E SNV was detected in 12.3% of cases. Larger tumor size and higher initial risk were associated with genetic alterations (P = 0.027 and P = 0. 036, respectively). Designing a laboratory algorithm following an increasing order of complexity provided a reliable molecular testing platform that reduces the requirement for NGS screening. These results also broaden the data on PTC alterations in children from Argentina.

Immune checkpoint expression and therapeutic implications in IDH1-mutant and wild-type glioblastomas

Programmed cell death protein 1 (PDCD1) and cluster of differentiation 274 (CD274) expression is implicated in escaping tumors from immune surveillance. Immune checkpoint inhibitors show promise in cancer therapy, yet their efficacy in glioblastomas, particularly with IDH1 mutations, remains unclear. This study analyzed two independent NGS datasets (n = 577 and n = 153) from TCGA to investigate the expression of PDCD1 and CD274 in glioblastomas and their relationship with IDH1 mutations. We used cBioPortal for mutation analysis, RNA seq for expression analysis, miRDB and miRabel for differential expression of miRNAs, and Kaplan-Meier for survival prediction. We found that 5.4% of glioblastomas harbored IDH1 mutations, correlating with improved overall survival (OS) (p = 2.196e-3). Different glioblastoma cohorts showed a diverse IDH1 mutational prevalence (4-31%). Despite this, IDH1Mu was consistently associated with better OS (p = 8.235e-5). Notably, PDCD1 and CD274 were statistically significantly highly expressed in both IDH1Wt (p < 0.0001) and IDH1Mu tumors (p < 0.0001), with higher expression linked to poorer survival outcomes (PDCD1: p = 0.009; CD274: p = 0.02). Differential co-expression analyses revealed distinct gene and miRNA profiles for IDH1Wt and IDH1Mu glioblastomas, with specific upregulation of PTEN and downregulation of MUC16 in IDH1Wt, and upregulation of PIK3R1 in IDH1Mu. Additionally, PIK3R1 and ITGB2 emerged as critical druggable targets. Our findings indicate that PDCD1 and CD274 are highly expressed irrespective of IDH1 mutation statuses, suggesting that glioblastomas could benefit from immunotherapy. Moreover, IDH1Mu glioblastomas may require a combination of PI3K/AKT/mTOR inhibitors and immunotherapy due to PIK3R1 overexpression.

Next generation sequence-based targeted somatic mutation analysis in thyroid nodules with pathologically diagnosed as indeterminate cytology

PURPOSE

The management of indeterminate thyroid nodules remains a topic of ongoing debate, particularly regarding the differentiation of malignancy. Somatic mutation analysis offers crucial insights into tumor characteristics. This study aimed to assist the clinical management of indeterminate nodules with somatic mutation analysis.

METHODS

Aspiration samples from 20 indeterminate thyroid nodules were included in the study. A next-generation sequencing panel containing 67 genes was used for molecular profiling. The results were compared with pathology data from surgical material, which is considered the gold standard. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated.

RESULTS

Variants in six genes (NRAS, BRAF, TP53, TERT, PTEN, PIK3CA) were detected in 10 out of 20 samples. We identified nine Tier 1 or 2 variants in 10 (67 %) out of 15 malignant nodules (NRAS, BRAF, TP53, TERT, PTEN, PIK3CA) and one Tier 2 (PIK3CA) variant in one out of five benign nodules. The study demonstrated an NPV of 40 %, a PPV of 90 %, a specificity of 80 %, and a sensitivity of 60 %.

CONCLUSION

Based on the detected molecular markers, at least nine patients (45 %) could be managed correctly without needing a repeat FNAB attempt. This study underscores the clinical practicality of molecular tests in managing nodules with indeterminate cytology. Additionally, this study emphasizes the importance of considering the patient's age when determining the DNA- or RNA-based genetic testing method. Finally, we discussed the significance of the somatic mutation profile and its impact on the current pathological classification.

LncRNA GAS8-AS1 dinucleotide genetic variantn.713A>G, n.714T>C is associated with early-stage disease, lymph node, and distant metastasis in differentiated thyroid cancer

PURPOSE

Long noncoding RNAs (lncRNAs) play an essential role in the epigenetic regulation of various key genes involved in vital cellular functions. A somatic dinucleotide mutation in the lncRNA GAS8-AS1 was reported in Chinese papillary thyroid cancer. However, GAS8-AS1 dinucleotide alteration and its impact have never been explored in differentiated thyroid cancers and other populations.

METHODS

We extracted genomic DNA from 265 DTCs and 97 normal healthy subjects, PCR amplified and Sanger sequenced to examine the GAS8-AS1 dinucleotide alteration. Calculated genotype/allele frequency to test Hardy-Weinberg Equilibrium (HWE) and performed a genetic model of inheritance to determine its association with DTC risk. Correlated the GAS8-AS1 dinucleotide variant distribution with clinical characteristics to find the association. Predicted GAS8-AS1 RNA secondary structure for wild type and variant using RemuRNA and RNAfold to assess the conformational changes.

RESULTS

GAS8-AS1 dinucleotide alteration (n.713A > G, rs55742939; n.714T > C, rs61118444) identified in DTCs is a germline variant not somatic. The GAS8-AS1 genotype and allele frequency significantly deviated for HWE in DTCs (χ2 = 37.954; p = 0.0001) though not associated with its risk. Dinucleotide variant distribution was remarkably associated with early-stage disease (p = 0.002), lymph node (p = 0.01), and distant metastasis (p = 0.01) in DTCs. The GAS8-AS1 bearing dinucleotide variant markedly showed conformational change compared to that of its wild type.

CONCLUSIONS

These findings indicate that GAS8-AS1 is genetically deregulated and implicated in several stages of DTC tumorigenesis suggesting it could be a promising prognostic biomarker in DTCs.

Histological evidence of MAPK pathway activation across subtypes of adult orbital xanthogranulomatous disease irrespective of the detection of oncogenic mutations

Adult orbital xanthogranulomatous disease (AOXGD) is a spectrum of histiocytoses with four subtypes. Mitogen-activated protein kinase (MAPK) pathway mutations have been detected in various histiocytic neoplasms, little is known about this in AOXGD. Targeted regions of cancer- and histiocytosis-related genes were analyzed and immunohistochemical staining of phosphorylated ERK (pERK), cyclin D1 and PU.1 was performed in 28 AOXGD and 10 control xanthelasma biopsies to assess MAPK pathway activation. Mutations were detected in 7/28 (25%) patients. Positive staining for pERK and/or cyclin D1 was found across all subtypes in 17/27 (63%) patients of whom 12/17 (71%) did not harbour a mutation. Xanthelasma tissue stained negative for pERK and cyclin D1. Relapse occurred in 5/7 (71%) patients with a MAPK pathway mutation compared to 8/21 (38%) patients in whom no mutation could be detected. Molecular analysis and evaluation for systemic disease is warranted to identify patients at risk of recurrent xanthomatous disease.

Analysis of ALK, IDH1, IDH2 and MMP8 somatic mutations in differentiated thyroid cancers

Anaplastic lymphoma kinase (ALK), isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) and matrix metalloproteinase 8 (MMP8) gene mutations have been frequently reported in human cancers; however, to the best of our knowledge, they have not been specifically examined in differentiated thyroid cancers (DTCs). Therefore, the present study aimed to determine the somatic mutational frequencies of these genes in DTCs. Mutational analysis of the ALK (exons 23, 24 and 25), IDH1 (exon 4), IDH2 (exon 4), and MMP8 (all exons 1-10) was performed in 126, 271, 271 and 50 DTCs, respectively. All the indicated exons were PCR-amplified and the PCR products were directly sequenced by Sanger sequencing. The present study identified a high frequency (86%; 43/50) of MMP8 single nucleotide polymorphism (SNP) and also found some rare SNPs of this gene (S3C, T32I, L310P and K460T) in DTCs but no somatic mutation in ALK, IDH1, IDH2 and MMP8. Analyses of 414 DTCs from The Cancer Genome Atlas revealed rare ALK (1%) and MMP8 (0.24%) mutations and none in IDH1 and IDH2. Conversely, analyses of 117 aggressive thyroid cancers [84, poorly differentiated thyroid cancer (PDTC); 33, anaplastic thyroid cancer (ATC)] from the Memorial Sloan Kettering Cancer Center cohort revealed ALK mutations in 3% of ATCs and fusions in 3.6% of PDTCs. IDH1 mutation was identified in 1.25% of PDTCs but not in ATC. IDH2 mutation was identified in 3% of ATCs but not in PDTC. The present study demonstrated that these genes are less frequently mutated in DTCs, but common in ATCs and PDTCs. It suggests that these genes serve a role in a small portion of DTCs and a more important role in ATCs and PDTCs and may serve as potential therapeutic targets in these subsets.