Intratumor BRAFV600E heterogeneity and kinase inhibitors in the treatment of thyroid cancer: a call for participation

Intra-tumor heterogeneity, turnover rate and karyotype space shape susceptibility to missegregation-induced extinction

The phenotypic efficacy of somatic copy number alterations (SCNAs) stems from their incidence per base pair of the genome, which is orders of magnitudes greater than that of point mutations. One mitotic event stands out in its potential to significantly change a cell's SCNA burden-a chromosome missegregation. A stochastic model of chromosome mis-segregations has been previously developed to describe the evolution of SCNAs of a single chromosome type. Building upon this work, we derive a general deterministic framework for modeling missegregations of multiple chromosome types. The framework offers flexibility to model intra-tumor heterogeneity in the SCNAs of all chromosomes, as well as in missegregation- and turnover rates. The model can be used to test how selection acts upon coexisting karyotypes over hundreds of generations. We use the model to calculate missegregation-induced population extinction (MIE) curves, that separate viable from non-viable populations as a function of their turnover- and missegregation rates. Turnover- and missegregation rates estimated from scRNA-seq data are then compared to theoretical predictions. We find convergence of theoretical and empirical results in both the location of MIE curves and the necessary conditions for MIE. When a dependency of missegregation rate on karyotype is introduced, karyotypes associated with low missegregation rates act as a stabilizing refuge, rendering MIE impossible unless turnover rates are exceedingly high. Intra-tumor heterogeneity, including heterogeneity in missegregation rates, increases as tumors progress, rendering MIE unlikely.

BRAFV600E Mutation: Has It a Role in Cervical Lymph Node Metastasis of Papillary Thyroid Cancer?

BACKGROUND

The BRAF^V600E mutation is common in papillary thyroid cancer (PTC). Lymph node metastasis (LNM) may be associated with poor prognosis. However, the LNM mechanism remains unclear.

OBJECTIVES

Our aim was to evaluate the prevalence of the BRAF^V600E mutation in primary tumors and accompanying LNM at the time of diagnosis.

METHODS

This retrospective study included 51 PTC patients (40 women, 11 men; mean age 40.0 ± 16.5 years; range 6-81) who underwent total thyroidectomy accompanied by a lateral neck dissection due to preoperatively detected LNM. Real-time PCR was used for the detection of the BRAF^V600E mutation in specimens from primary thyroid tumors and metastatic lymph node tumors.

RESULTS

The prevalence of the BRAF^V600E mutation was 64.7% (n = 33) in primary tumors and 47.1% (n = 24) in metastatic lymph nodes. Of 33 patients with BRAF^V600E-positive primary tumors, 18 (54.5%) had BRAF^V600E-positive metastatic lymph nodes. Of 18 patients with BRAF^V600E-negative primary tumors, 6 (33.3%) had BRAF^V600E-positive metastatic lymph nodes. The presence of the BRAF^V600E mutation in the primary tumor did not affect the tumor size, but the diameter of metastatic lymph nodes significantly increased (by nearly 3 mm) with the presence of BRAF^V600E in LNM (p = 0.01).

CONCLUSIONS

In our study, the BRAF^V600E mutation did not show a one-to-one correspondence. This indicates that the presence of BRAF^V600E in the primary tumor is not clonal and addresses the role of intratumor heterogeneity in PTC tumorigenesis. This supports the theses that mutations occur in the later stages of tumorigenesis, might be subclonal, and develop de novo, or that some other factors may be involved in the development of metastasis.

Benign thyroid nodules with RAS mutation grow faster

CONTEXT

The management of a benign thyroid nodule includes follow-up until its size requires a surgical or alternative treatment. To date, it is difficult or impossible to predict the size changes of a benign nodule in a given patient because no specific growth parameters exist. RAS mutations have been described in thyroid adenomas and hyperplastic benign nodules.

OBJECTIVE

The aim of this study was to establish whether the volume changes of benign nodules are associated with the presence of RAS mutation.

PATIENTS AND METHODS

Genomic DNA obtained by fine-needle aspiration of 78 thyroid nodules with benign cytology was analysed by pyrosequencing for the presence of NRAS(61) and KRAS(13) mutations. Ultrasonographic features were obtained. The volume of nodules at baseline and their changes after a mean follow-up of 25 months were evaluated according to the presence of RAS mutation.

RESULTS

A RAS mutation was found in 24 thyroid aspirates (30·8%, 8 NRAS(61) and 16 KRAS(13) ). RAS mutation was not associated with ultrasonographic features, but was significantly associated with a larger size at baseline (P = 0·017). After a 25-month mean follow-up, RAS mutation-positive nodules displayed faster growth (RAS mutation-positive vs RAS mutation-negative % annual growth 27·6% ±32·2% vs 1·0% ±17·0%, P < 0·001).

CONCLUSIONS

Benign thyroid nodules bearing RAS mutation grow more rapidly than those with wild-type RAS. Searching for RAS mutations in thyroid nodules with benign cytology might be useful to the clinician in choosing a more appropriate and timely surgical management.

Heterogeneity in Melanoma

Melanoma is among the most aggressive and therapy-resistant human cancers. While great strides in therapy have generated enthusiasm, many challenges remain. Heterogeneity is the most pressing issue for all types of therapy. This chapter summarizes the clinical classification of melanoma, of which the research community now adds additional layers of classifications for better diagnosis and prediction of therapy response. As the search for new biomarkers increases, we expect that biomarker analyses will be essential for all clinical trials to better select patient populations for optimal therapy. While individualized therapy that is based on extensive biomarker analyses is an option, we expect in the future genetic and biologic biomarkers will allow grouping of melanomas in such a way that we can predict therapy outcome. At this time, tumor heterogeneity continues to be the major challenge leading inevitably to relapse. To address heterogeneity therapeutically, we need to develop complex therapies that eliminate the bulk of the tumor and, at the same time, the critical subpopulations.

Surgical management of cervico-mediastinal goiters: Our experience and review of the literature

AIM

We analyze and discuss the clinical presentation, the diagnostic procedures and the surgical technique in relation to post-operative complications and results in cervico-mediastinal thyroid masses admitted in Thoracic Surgery Unit of AOU Second University of Naples from 1991 to 2006 and in Thoracic Surgery Unit of AOU "S. Giovanni di Dio & Ruggi D'Aragona" of Salerno over a period of 3 years (2011-2014).

METHODS

We reviewed 97 patients who underwent surgical treatment for cervico-mediastinal goiters. 47 patients (49.2%) had cervico-mediastinal goiter, 40 patients (40%) had mediastino-cervical goiter and 10 patients (10.8%) had mediastinal goiter. 73 cases were prevascular goiters and 24 were retrovascular goiters. We performed total thyroidectomy in 40 patients, subtotal thyroidectomy in 46 patients and in 11 cases the resection of residual goiter. In 75 patients we used only a cervical approach, in 21 patients the cervical incision was combined with median sternotomy and in 1 patient with transverse sternotomy.

RESULTS

Three patients (3.1%) died in the postoperative period (2 cardio-respiratory failure and 1 pulmonary embolism). The histologic study revelead 8 (7.7%) carcinomas. Postoperative complications were: dyspnea in 9 cases (10.7%), transient vocal cord paralysis in 6 patients (9.2%), temporary hypoparathyroidism in 9 patients (9.2%) and kidney failure in 1 case (0.9%).

CONCLUSIONS

The presence of a cervico-mediastinal thyroid mass with or without respiratory distress requires a surgical excision as the only treatment option. Thyroid masses extending to the mediastinum can be excised successfully by cervical incision. Bipolar approach (cervical incision and sternotomy) has an excellent outcome, achieving a safe resection, especially in large thyroid masses extending to the mediastinum with close relations to mediastinal structures and in some limited cases (carcinoma, thyroiditis, retrovascular goiter, ectopic goiter). Postoperative mortality and morbidity is very low, independent of surgical techniques. Other surgical approaches for excision of a Posterior Mediastinal Thyroid Goiter reported in literature are: VATS techniques to remove an ectopic intrathoracic goiter, robot-assisted technique for the removal of a substernal thyroid goiter, with extension into the posterior mediastinum.

Pan-cancer analysis of the extent and consequences of intratumor heterogeneity

Intratumor heterogeneity (ITH) drives neoplastic progression and therapeutic resistance. We used the bioinformatics tools 'expanding ploidy and allele frequency on nested subpopulations' (EXPANDS) and PyClone to detect clones that are present at a ≥10% frequency in 1,165 exome sequences from tumors in The Cancer Genome Atlas. 86% of tumors across 12 cancer types had at least two clones. ITH in the morphology of nuclei was associated with genetic ITH (Spearman's correlation coefficient, ρ = 0.24-0.41; P < 0.001). Mutation of a driver gene that typically appears in smaller clones was a survival risk factor (hazard ratio (HR) = 2.15, 95% confidence interval (CI): 1.71-2.69). The risk of mortality also increased when >2 clones coexisted in the same tumor sample (HR = 1.49, 95% CI: 1.20-1.87). In two independent data sets, copy-number alterations affecting either <25% or >75% of a tumor's genome predicted reduced risk (HR = 0.15, 95% CI: 0.08-0.29). Mortality risk also declined when >4 clones coexisted in the sample, suggesting a trade-off between the costs and benefits of genomic instability. ITH and genomic instability thus have the potential to be useful measures that can universally be applied to all cancers.

Detection of RAS mutation by pyrosequencing in thyroid cytology samples

INTRODUCTION

Fine-needle aspiration cytology (FNAC) is the primary means to distinguish benign from malignant thyroid nodules. However, adjunctive diagnostic tests are needed as 20-40% of FNAC are inconclusive. RAS mutations have been described in differentiated thyroid cancer and they could be used as tumor markers. However, their prevalence varies widely among studies, probably as a result of the detection methods used. We investigated whether the pyrosequencing method can be applied to detect NRAS and KRAS mutations in thyroid aspirates.

PATIENTS AND METHODS

A total of 37 thyroid aspirates, including benign hyperplastic nodules (HBN, N = 16) and follicular thyroid carcinomas (FTC, N = 21) were analyzed for the presence of NRAS(61) and KRAS(13) mutations.

RESULTS

A RAS mutation was found in 31% and 62% of BN and FTC respectively. Most samples displayed a percentage of mutated alleles lower than 50% (median = 30.8% and 15.3% in FTC and HBN respectively), a result compatible with the presence of extra-nodular cells contaminating the FNA or with the subclonal nature of both types of thyroid nodules.

DISCUSSION

Pyrosequencing is a reliable assay to detect RAS mutations in fine-needle thyroid aspirates.

CONCLUSIONS

The low specificity and sensitivity limit the power of this test to distinguish between FTC and benign nodules in inconclusive FNACs.

BRAF(V600E) assessment by pyrosequencing in fine needle aspirates of thyroid nodules with concurrent Hashimoto's thyroiditis is a reliable assay

Detection of BRAF mutation in cytology specimens has been proposed as a diagnostic adjunctive tool in evaluation of thyroid nodules with indeterminate cytology findings. Concurrent papillary thyroid carcinoma and Hashimoto's thyroiditis (HT), a disease characterized by thyroid lymphocytic infiltration, is a frequent occurrence. A large lymphocytic infiltrate might reduce the sensitivity of methods employed to detect BRAF mutation in thyroid cytology specimens. To determine whether testing for BRAF mutational status in fine needle aspirates (FNA) is reliable also in the presence of HT lymphocytic infiltration, we assessed the BRAF status by direct sequencing and pyrosequencing in a series of FNAs with and without concomitant HT lymphocytic infiltration. We also performed the same assessment by pyrosequencing in the corresponding tissue samples. Pyrosequencing demonstrated to be more sensitive than direct sequencing. The percentage of mutant BRAF(V600E) alleles was higher in FNAs than in the corresponding tissues, probably because of the lower stromal contamination in FNA than in the sections. In the presence of lymphocytic infiltration, the percentage of mutant BRAF(V600E) alleles determined by pyrosequencing was higher in FNAs than in the corresponding tissue samples (P < 0.0001), indicating a minor lymphocytic contamination in FNA. The diagnostic value of BRAF(V600E) in inconclusive FNAs was not hampered by thyroid lymphocytic infiltration. These results indicate that BRAF(V600E) assessment by pyrosequencing is a reliable assay useful to refine inconclusive cytology of thyroid nodules also in the presence of concurrent HT.

Optimizing detection of RET and PPARg rearrangements in thyroid neoplastic cells using a home-brew tetracolor probe

BACKGROUND

Fluorescence in situ hybridization (FISH) to identify specific DNA target sequences in the nuclei of nondividing cells of numerous solid neoplasms has contributed to the introduction of molecular cytogenetics as a useful adjunct to cytology, leading recently to the "marriage" of the 2 disciplines. Numerous cancer molecular markers can now be investigated using different technical approaches, at both the gene and expression levels, in biopsies of various suspected cancers, including differentiated thyroid carcinoma. The limited amount of bioptic material is often insufficient to carry out multiple tests, and optimizing handling of the biopsy is desirable.

METHODS

We have developed a home-brew tetracolor break-apart probe able to simultaneously identify the 2 most common genetic alterations in differentiated thyroid carcinoma: RET/PTC variants in papillary thyroid carcinoma and PAX8/PPARg fusion and variants in follicular thyroid carcinoma.

RESULTS

The probe had 100% specificity, 99.5% sensitivity, and ≥ 3% cutoff. The probe was tested on RET/PTC and PAX8/PPARg RT-PCR positive controls, and feasibility was assessed in 368 thyroid nodule fine-needle aspirations (FNA). In the latter analysis, 24 FNAs had split RET signal, and 9 had split PPARg signal. FISH analysis of available surgically removed nodules confirmed the sensitivity of FISH in detecting abnormal clones and oligoclones.

CONCLUSIONS

The home-brew tetracolor probe showed high feasibility, optimizing the use of the biological material in relation to the available molecular tests and maximizing the FISH experimental and slide-scoring times. This probe may be considered an alternative to RT-PCR when recovery and quality of RNA amplification from FNA are insufficient.

Concomitant BRAF(V600E) mutation and RET/PTC rearrangement is a frequent occurrence in papillary thyroid carcinoma

BACKGROUND

The tyrosine kinase receptors/RAS/RAF/MAPK cascade is a site of mutational events associated with thyroid carcinogenesis. Some studies suggest the reciprocal exclusion of different oncogenes in the mitogen-activated protein kinase cascade, whereas others suggest that BRAF mutations and RET rearrangements can simultaneously occur in sporadic cases. The aim of this study was to determine the prevalence of concomitant BRAF(V600E) mutation and RET/PTC rearrangements in the same tumor and its association with some clinicopathological features.

METHODS

The percentage of mutant BRAF alleles and the presence of RET/PTC rearrangements were determined by means of pyrosequencing and Southern blot analysis of reverse transcription polymerase chain reaction products in a series of 72 conventional papillary thyroid carcinomas (PTCs). Then, the associations between clinicopathological characteristics and mutation status were assessed.

RESULTS

BRAF(V600E) alleles were present in 32 out of 72 PTCs (44.4%) in the range of 5.1-44.7% of total BRAF alleles. RET/PTC was present in 26 tumors (36.1%). Concomitant subclonal BRAF and RET/PTC were demonstrated in 14 PTCs (19.4%), and none of the oncogenes was detected in 22 tumors (30.5%). Only BRAF(V600E) was associated with a more advanced tumor staging.

CONCLUSIONS

The present study demonstrates that concomitant BRAF mutation and RET/PTC rearrangement is a frequent event in PTC.

Radioiodide induces apoptosis in human thyroid tissue in culture

Radioiodide ((131)I) is routinely used for the treatment of toxic adenoma, Graves' disease, and for ablation of thyroid remnant after thyroidectomy in patients with thyroid cancer. The toxic effects of ionizing radiations on living cells can be mediated by a necrotic and/or apoptotic process. The involvement of apoptosis in radiation-induced cell death in the thyrocytes has been questioned. The knowledge of the mechanisms that underlie the thyrocyte death in response to radiations can help to achieve a successful treatment with the lowest (131)I dose. We developed a method to study the effects of (131)I in human thyroid tissue in culture, by which we demonstrated that (131)I induces thyroid cell apoptosis. Human thyroid tissues of about 1 mm(3) were cultured in vitro and cell viability was determined up to 3 weeks by the MTT assay. Radioiodide added to the culture medium was actively taken up by the tissues. The occurrence of apoptosis in the thyrocytes was assessed by measuring the production of a caspase-cleavage fragment of cytokeratin 18 (M30) by an enzyme-linked immunoassay. Neither variation of cell number nor spontaneous apoptosis was revealed after 1 week of culture. (131)I added to the culture medium induced a dose-dependent and a time-dependent generation of M30 fragment. The apoptotic process was confirmed by the generation of caspase-3 and PARP cleavage products. These results demonstrate that (131)I induces apoptosis in human thyrocytes. Human thyroid tissue cultures may be useful to investigate the cell death pathways induced by (131)I.

Genetic mutations in the treatment of anaplastic thyroid cancer: a systematic review

BACKGROUND

Anaplastic thyroid cancer (ATC) is a rare, lethal disease associated with a median survival of 6 months despite the best multidisciplinary care. Surgical resection is not curative in ATC patients, being often a palliative procedure. Multidisciplinary care may include surgery, loco-regional radiotherapy, and systemic therapy. Besides conventional chemotherapy, multi kinase-targeted inhibitors are emerging as novel therapeutic tools. The numerous molecular alteration detected in ATC are targets for these inhibitors. The aim of this review is to determine the prevalence of the major genetic alterations occurring in ATC and place the results in the context of the emerging kinase-targeted therapies.

METHODS

The study is based on published PubMed studies addressing the prevalence of BRAF, RAS, PTEN, PI3KCA and TP53 mutations and RET rearrangements in ATC.

RESULTS

21 articles dealing with 652 genetic analyses of the selected genes were used. The overall prevalence determined were the following: RET/PTC, 4%; BRAF, 23%; RAS, 60%; PTEN, 16%; PI3KCA, 24%; TP53, 48%. Genetic alterations are sometimes overlapping.

CONCLUSIONS

Mutations of BRAF, PTEN and PI3KCA genes are common in ATC, with RAS and TP53 being the most frequent. Given ATC genetic complexity, effective therapies may benefit from individualized therapeutic regimens in a multidisciplinary approach.

Nodular goiter with amyloid deposition in an elderly patient: fine-needle cytology diagnosis and review of the literature

Background

Amyloidosis is a systemic disease characterized by the extracellular deposition of amyloid fibrils in different organs and tissues. The thyroid gland may be affected by diffuse or nodular amyloid deposits, along with multiple myeloma (MM) (Amyloid Light-Chain Amyloidosis, AL amyloidosis) or chronic inflammatory diseases (Amyloid A Amyloidosis, AA amyloidosis), but thyroid gland involvement rarely appears as the first clinical manifestation in both conditions. The present study reports a case of primary thyroidal nodular amyloid goiter diagnosed by fine-needle cytology (FNC) in an elderly patient.

Case report

A 66-year-old female patient presented with dysphagia and hoarseness; the patient suffered from rheumatoid arthritis but did not have kidney failure or altered thyroid function. Ultrasound examination (US) showed a 30 mm irregular, hypoechoic area in the left thyroid lobe. FNC showed abundant, dense and amorphous material similar to the one stained in purple at Diff-Quik stain and pinkish at the Papanicolaou. Spindle cells with thin, bland and bent nuclei were scattered in this material; few thyroid follicular cells were also present. An alcohol-fixed smear was stained with Congo red: the amyloid material appeared cherry red and it also showed apple-green birefringence when observed with a polarizing microscope. A differential diagnosis between different thyroid pathologies was considered and the cytological diagnosis of nodular amyloid goiter was pointed out. The patient underwent thyroid lobectomy and the subsequent histological examination confirmed the cytological diagnosis.

Conclusions

FNC is a safe and effective procedure for the diagnosis of thyroid amyloidosis. Congo red-stained smears can be used to demonstrate the presence of amyloid material, showing the typical green birefringence under polarized light. An early and accurate cytological diagnosis may suggest an hematological screening and the appropriate treatment for the thyroid nodule.

Early cytological diagnosis of extranodal stage I, primary thyroid Non-Hodgkin lymphoma in elderly patients. Report of two cases and review of the literature

Background

Primary thyroid lymphomas (PTLs) account for 5% of thyroid malignant tumors and often develop in patients with Hashimoto Thyroiditis (HT). Fine-needle cytology (FNC) is widely used in the diagnosis of thyroid nodules, including those arising in HT. Two PTL cases in HT elderly patients are here described and discussed.

Methods

FNC was performed in rapidly enlarged thyroid nodules of 2 elderly patients under ultrasound (US) control. FNC was used to prepare conventional cytologic smears, immunocytochemistry (ICC) and flow cytometry (FC) assessment of cell populations.

Results

The above cases were diagnosed as well differentiated, small B-cell and diffuse large B-cell thyroid lymphomas, respectively, by means of FNC. The histological diagnoses were mucosa-associated non Hodgkin lymphoma (MALT) and diffuse large B-cell lymphoma (DLBCL), confirming FNC diagnoses, and patients were treated accordingly.

Conclusions

FNC diagnosis of PTL is reliable and accurate; it may be conveniently used in the clinical practice since it provides indications for appropriate therapeutic procedures or diagnostic surgery, and avoids to treat benign nodules.

Diagnostic utility of BRAFV600E mutation testing in thyroid nodules in elderly patients

Background

Thyroid cancer is a rare disease characterized by the subtle appearance of a nodule. Fine-needle cytology (FNC) is the first diagnostic procedure used to distinguish a benign from a malignant nodule. However, FNC yields inconclusive results in about 20% of cases. BRAF^V600E mutation is the most frequent genetic alteration in papillary thyroid carcinoma (PTC); its high prevalence makes this oncogene a useful marker to refine inconclusive FNC results. However, the prevalence of the BRAF^V600E mutation depends on detection methods, geographical factors, and age. The aim of this study is to determine the prevalence of BRAF^V600E mutation and its utility as a diagnostic tool in elderly subjects.

Methods

FNC from 92 PTC patients were subjected to the analysis of BRAF mutation by pyrosequencing and direct sequencing; age-dependent prevalence was also determined.

Results

BRAF mutation analysis was successful in all FNC specimens. BRAF^V600E was documented in 62 (67.4%) and in 58 (63.0%) PTCs by pyrosequencing and direct sequencing, respectively. BRAF^V600E prevalence did not correlate with patient's age at diagnosis. Twenty out of 32 PTCs (62.5%) were correctly diagnosed by BRAF mutation analysis in inconclusive FNC results.

Conclusions

Detection of BRAF^V600E in cytology specimens by pyrosequencing is a useful diagnostic adjunctive tool in the evaluation of thyroid nodules also in elderly subjects.