Intratumor heterogeneity and clonal evolution in an aggressive papillary thyroid cancer and matched metastases

Significance of Distinct Liquid Biopsy Compartments in Evaluating Somatic Mutations for Targeted Therapy Selection in Cancer of Unknown Primary

PURPOSE

Cancer of unknown primary (CUP) accounts for 2-5% of all cancer diagnoses, wherein standard investigations fail to reveal the original tumor site. Basket trials allocate targeted therapeutics based on actionable somatic mutations, independent of tumor entity. These trials, however, mostly rely on variants identified in tissue biopsies. Since liquid biopsies (LB) represent the overall tumor genomic landscape, they may provide an ideal diagnostic source in CUP patients. To identify the most informative liquid biopsy compartment, we compared the utility of genomic variant analysis for therapy stratification in two LB compartments (circulating cell-free (cf) and extracellular vesicle (ev) DNA).

METHODS

CfDNA and evDNA from 23 CUP patients were analyzed using a targeted gene panel covering 151 genes. Identified genetic variants were interpreted regarding diagnostic and therapeutic relevance using the MetaKB knowledgebase.

RESULTS

LB revealed a total of 22 somatic mutations in evDNA and/or cfDNA in 11/23 patients. Out of the 22 identified somatic variants, 14 are classified as Tier I druggable somatic variants. Comparison of variants identified in evDNA and cfDNA revealed an overlap of 58% of somatic variants in both LB compartments, whereas over 40% of variants were only found in one or the other compartment.

CONCLUSION

We observed substantial overlap between somatic variants identified in evDNA and cfDNA of CUP patients. Nonetheless, interrogation of both LB compartments can potentially increase the rate of druggable alterations, stressing the significance of liquid biopsies for possible primary-independent basket and umbrella trial inclusion.

Metastatic differentiated thyroid cancer with negative serum stimulated Tg but positive post-therapeutic 131I-SPECT/CT scintigraphy: a single-center retrospective study

PURPOSE

This study aimed to describe the characteristics of patients with metastatic differentiated thyroid carcinoma (DTC) who had positive 131I-scintigraphy but negative stimulated thyroglobulin (sTg), and to evaluate their short-term response to radioiodine therapy (RAI).

METHODS

A total of 2250 consecutive postoperative DTC patients, who underwent RAI treatment from July 2019 to June 2022, were analyzed retrospectively. The target group was defined as stimulated Tg < 2 ng/mL with TgAb < 100 IU/mL but with post-therapeutic 131I-SPECT/CT metastases. The characteristics of these patients were analyzed and the metastatic profiles were compared with TgAb positive or sTg positive ones. A cross-sectional efficacy was evaluated 6-12 months after the RAI therapy and the treatment course until the end of the study was recorded.

RESULTS

105 (4.67%) DTC patients were post-therapeutic 131I-SPECT/CT positive and sTg negative (target group). Metastatic profiles were found significant differences between sTg negative and sTg positive ones (P < 0.001). Excellent response (ER) was achieved in 72.4% of the target group between 6-12 months of cross-sectional efficacy assessment, compared with only 12.8% in sTg positive ones (P < 0.001). The majority of the target group didn't require aggressive treatment in short-term follow-up compared with sTg positive group (P < 0.001).

CONCLUSION

The percentage of DTCs with negative sTg but positive post-therapeutic 131I-SPECT/CT was relatively low, but still significant. Moreover, the majority of these patients showed an ER to RAI and may not require the next course of therapy. Long-term follow-up is still necessary to assess recurrence and adapt surveillance in these patients.

DNA methylation profile in CpG-depleted regions uncovers a high-risk subtype of early-stage colorectal cancer

BACKGROUND

The current risk stratification system defined by clinicopathological features does not identify the risk of recurrence in early-stage (stage I-II) colorectal cancer (CRC) with sufficient accuracy. We aimed to investigate whether DNA methylation could serve as a novel biomarker for predicting prognosis in early-stage CRC patients.

METHODS

We analyzed the genome-wide methylation status of CpG loci using Infinium MethylationEPIC array run on primary tumor tissues and normal mucosa of early-stage CRC patients to identify potential methylation markers for prognosis. The machine-learning approach was applied to construct a DNA methylation-based prognostic classifier for early-stage CRC (MePEC) using the 4 gene methylation markers FAT3, KAZN, TLE4, and DUSP3. The prognostic value of the classifier was evaluated in 2 independent cohorts (n = 438 and 359, respectively).

RESULTS

The comprehensive analysis identified an epigenetic subtype with high risk of recurrence based on a group of CpG loci in the CpG-depleted region. In multivariable analysis, the MePEC classifier was independently and statistically significantly associated with time to recurrence in validation cohort 1 (hazard ratio = 2.35, 95% confidence interval = 1.47 to 3.76, P < .001) and cohort 2 (hazard ratio = 3.20, 95% confidence interval = 1.92 to 5.33, P < .001). All results were further confirmed after each cohort was stratified by clinicopathological variables and molecular subtypes.

CONCLUSIONS

We demonstrated the prognostic statistical significance of a DNA methylation profile in the CpG-depleted region, which may serve as a valuable source for tumor biomarkers. MePEC could identify an epigenetic subtype with high risk of recurrence and improve the prognostic accuracy of current clinical variables in early-stage CRC.

Papillary thyroid cancer organoids harboring BRAFV600E mutation reveal potentially beneficial effects of BRAF inhibitor-based combination therapies

BACKGROUNDS

Papillary thyroid cancer (PTC), which is often driven by acquired somatic mutations in BRAF genes, is the most common pathologic type of thyroid cancer. PTC has an excellent prognosis after treatment with conventional therapies such as surgical resection, thyroid hormone therapy and adjuvant radioactive iodine therapy. Unfortunately, about 20% of patients develop regional recurrence or distant metastasis, making targeted therapeutics an important treatment option. Current in vitro PTC models are limited in representing the cellular and mutational characteristics of parental tumors. A clinically relevant tool that predicts the efficacy of therapy for individuals is urgently needed.

METHODS

Surgically removed PTC tissue samples were dissociated, plated into Matrigel, and cultured to generate organoids. PTC organoids were subsequently subjected to histological analysis, DNA sequencing, and drug sensitivity assays, respectively.

RESULTS

We established 9 patient-derived PTC organoid models, 5 of which harbor BRAF^V600E mutation. These organoids have been cultured stably for more than 3 months and closely recapitulated the histological architectures as well as mutational landscapes of the respective primary tumors. Drug sensitivity assays of PTC organoid cultures demonstrated the intra- and inter-patient specific drug responses. BRAF^V600E inhibitors, vemurafenib and dabrafenib monotherapy was mildly effective in treating BRAF^V600E-mutant PTC organoids. Nevertheless, BRAF inhibitors in combination with MEK inhibitors, RTK inhibitors, or chemotherapeutic agents demonstrated improved efficacy compared to BRAF inhibition alone.

CONCLUSIONS

These data indicate that patient-derived PTC organoids may be a powerful research tool to investigate tumor biology and drug responsiveness, thus being useful to validate or discover targeted drug combinations.

Unexpected Widespread Bone Metastases from a BRAF K601N Mutated Follicular Thyroid Carcinoma within a Previously Resected Multinodular Goiter

Follicular thyroid carcinoma (FTC) represents the second most common malignant thyroid neoplasm after papillary carcinoma (PTC). FTC is characterized by the tendency to metastasize to distant sites such as bone and lung. In the last 20 years, the understanding of the molecular pathology of thyroid tumors has greatly improved. Uncommon BRAF non-V600E mutations have been identified and are generally believed to associate with follicular patterned tumors of low malignant potential, particularly non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTPs) (i.e., non-invasive encapsulated follicular variant PTC). We here report for the first time widespread bone metastases from a BRAF K601N mutated follicular tumor.

Inflammatory Components of the Thyroid Cancer Microenvironment: An Avenue for Identification of Novel Biomarkers

The incidence of thyroid cancer in the United States is on the rise with an appreciably high disease recurrence rate of 20-30%. Anaplastic thyroid cancer (ATC), although rare in occurrence, is an aggressive form of cancer with limited treatment options and bleak cure rates. This chapter uses discussions of in vitro models that are representative of papillary, anaplastic, and follicular thyroid cancer to evaluate the crosstalk between specific cells of the tumor microenvironment (TME), which serves as a highly heterogeneous realm of signaling cascades and metabolism that are associated with tumorigenesis. The cellular constituents of the TME carry out varying characteristic immunomodulatory functions that are discussed throughout this chapter. The aforementioned cell types include cancer-associated fibroblasts (CAFs), endothelial cells (ECs), and cancer stem cells (CSCs), as well as specific immune cells, including natural killer (NK) cells, dendritic cells (DCs), mast cells, T regulatory (Treg) cells, CD8+ T cells, and tumor-associated macrophages (TAMs). TAM-mediated inflammation is associated with a poor prognosis of thyroid cancer, and the molecular basis of the cellular crosstalk between macrophages and thyroid cancer cells with respect to inducing a metastatic phenotype is not yet known. The dynamic nature of the physiological transition to pathological metastatic phenotypes when establishing the TME encompasses a wide range of characteristics that are further explored within this chapter, including the roles of somatic mutations and epigenetic alterations that drive the genetic heterogeneity of cancer cells, allowing for selective advantages that aid in their proliferation. Induction of these proliferating cells is typically accomplished through inflammatory induction, whereby chronic inflammation sets up a constant physiological state of inflammatory cell recruitment. The secretions of these inflammatory cells can alter the genetic makeup of proliferating cells, which can in turn, promote tumor growth.This chapter also presents an in-depth analysis of molecular interactions within the TME, including secretory cytokines and exosomes. Since the exosomal cargo of a cell is a reflection and fingerprint of the originating parental cells, the profiling of exosomal miRNA derived from thyroid cancer cells and macrophages in the TME may serve as an important step in biomarker discovery. Identification of a distinct set of tumor suppressive miRNAs downregulated in ATC-secreted exosomes indicates their role in the regulation of tumor suppressive genes that may increase the metastatic propensity of ATC. Additionally, the high expression of pro-inflammatory cytokines in studies looking at thyroid cancer and activated macrophage conditioned media suggests the existence of an inflammatory TME in thyroid cancer. New findings are suggestive of the presence of a metastatic niche in ATC tissues that is influenced by thyroid tumor microenvironment secretome-induced epithelial to mesenchymal transition (EMT), mediated by a reciprocal interaction between the pro-inflammatory M1 macrophages and the thyroid cancer cells. Thus, targeting the metastatic thyroid carcinoma microenvironment could offer potential therapeutic benefits and should be explored further in preclinical and translational models of human metastatic thyroid cancer.

Genomic and clinical findings in myeloid neoplasms with PDGFRB rearrangement

Platelet-derived growth factor receptor B (PDGFRB) gene rearrangements define a unique subgroup of myeloid and lymphoid neoplasms frequently associated with eosinophilia and characterized by high sensitivity to tyrosine kinase inhibition. To date, various PDGFRB/5q32 rearrangements, involving at least 40 fusion partners, have been reported. However, information on genomic and clinical features accompanying rearrangements of PDGFRB is still scarce. Here, we characterized a series of 14 cases with a myeloid neoplasm using cytogenetic, single nucleotide polymorphism array, and next-generation sequencing. We identified nine PDGFRB translocation partners, including the KAZN gene at 1p36.21 as a novel partner in a previously undescribed t(1;5)(p36;q33) chromosome change. In all cases, the PDGFRB recombination was the sole cytogenetic abnormality underlying the phenotype. Acquired somatic variants were mainly found in clinically aggressive diseases and involved epigenetic genes (TET2, DNMT3A, ASXL1), transcription factors (RUNX1 and CEBPA), and signaling modulators (HRAS). By using both cytogenetic and nested PCR monitoring to evaluate response to imatinib, we found that, in non-AML cases, a low dosage (100–200 mg) is sufficient to induce and maintain longstanding hematological, cytogenetic, and molecular remissions.

Targeting transcriptional regulators for treatment of anaplastic thyroid cancer

Dysregulation of genes perpetuates cancer progression. During carcinogenesis, cancer cells acquire dependency of aberrant transcriptional programs (known as “transcription addiction”) to meet the high demands for uncontrolled proliferation. The needs for particular transcription programs for cancer growth could be cancer-type-selective. The dependencies of certain transcription regulators could be exploited for therapeutic benefits. Anaplastic thyroid cancer (ATC) is an extremely aggressive human cancer for which new treatment modalities are urgently needed. Its resistance to conventional treatments and the lack of therapeutic options for improving survival might have been attributed to extensive genetic heterogeneity due to subsequent evolving genetic alterations and clonal selections during carcinogenesis. Despite this genetic complexity, mounting evidence has revealed a characteristic transcriptional addiction of ATC cells resulting in evolving diverse oncogenic signaling for cancer cell survival. The transcriptional addiction has presented a huge challenge for effective targeting as shown by the failure of previous targeted therapies. However, an emerging notion is that many different oncogenic signaling pathways activated by multiple upstream driver mutations might ultimately converge on the transcriptional responses, which would provide an opportunity to target transcriptional regulators for treatment of ATC. Here, we review the current understanding of how genetic alterations in cancer distorted the transcription program, leading to acquisition of transcriptional addiction. We also highlight recent findings from studies aiming to exploit the opportunity for targeting transcription regulators as potential therapeutics for ATC.

Organoid Cultures Derived From Patients With Papillary Thyroid Cancer

CONTEXT

Papillary thyroid cancer (PTC) has been one of the most frequent endocrine malignancies around the world. Although most PTC patients have a favorable prognosis, a subgroup of patients die, especially when disease recurrence occurs. There is a pressing need for clinically relevant preclinical thyroid cancer models for personalized therapy because of the lack of in vitro models that faithfully represent the biology of the parental tumors.

OBJECTIVE

To understand thyroid cancer and translate this knowledge to clinical applications, patient-derived PTC organoids as a promising new preclinical model were established.

METHODS

Surgically resected PTC primary tissues were dissociated and processed for organoid derivation. Tumor organoids were subsequently subjected to histological characterization, DNA sequencing, drug screen, and cell proliferation assay, respectively.

RESULTS

We describe a 3-dimensional culture system for the long-term expansion of patient-derived PTC organoid lines. Notably, PTC organoids preserve the histopathological profiles and genomic heterogeneity of the originating tumors. Drug sensitivity assays of PTC organoids demonstrate patient-specific drug responses, and large correlations with the respective mutational profiles. Estradiol was shown to promote cell proliferation of PTC organoids in the presence of estrogen receptor α (ERα), regardless of the expression of ERβ and G protein-coupled ER.

CONCLUSION

These data suggest that these newly developed PTC-derived organoids may be an excellent preclinical model for studying clinical response to anticancer drugs in a personalized way, as well as provide a potential strategy to develop prevention and treatment options for thyroid cancer with ERα-specific antagonists.

Intratumoral Heterogeneity in Differentiated Thyroid Tumors: An Intriguing Reappraisal in the Era of Personalized Medicine

Differentiated thyroid tumors (DTTs) are characterized by significant molecular variability in both spatial and temporal intra-tumoral heterogeneity (ITH), that could influence the therapeutic management. ITH phenomenon appears to have a relevant role in tumor growth, aggressive behavior and drug resistance. Accordingly, characteristics and consequences of ITH in DTTs should be better analyzed and understood in order to guide clinical practice, improving survival. Consequently, in the present review, we investigated morphological and molecular ITH of DTTs in benign, borderline neoplasms and in malignant entities, summarizing the most significant data. Molecular testing in DTTs documents a high risk for recurrence of cancer associated with BRAF^V600E, RET/PTC 1/3, ALK and NTRK fusions, while the intermediate risk may be related to BRAF^K601E, H/K/N RAS and PAX8/PPARγ. In addition, it may be suggested that tumor genotype is associated with peculiar phenotype.

Silencing of LINC00284 inhibits cell proliferation and migration in oral squamous cell carcinoma by the miR-211-3p/MAFG axis and FUS/KAZN axis

Oral squamous cell carcinoma (OSCC) is one of the most common malignancies worldwide. Emerging evidence has suggested that long noncoding RNAs (lncRNAs) play vital roles in various biological processes of cancers, such as cell proliferation, migration, invasion, and apoptosis. As reported previously, long intergenic non-protein coding RNA 284 (LINC00284) is an important regulator in multiple cancers. However, the biological role, as well as regulatory mechanism of LINC00284 in OSCC, has not been investigated. In our study, RT-qPCR results indicated that LINC00284 was significantly upregulated in OSCC tissues and cells. Moreover, loss-of-function experiments demonstrated that LINC00284 downregulation suppressed cell proliferation and migration and facilitated cell apoptosis. Mechanistically, we found that LINC00284 sponged microRNA 211-3p (miR-211-3p) to upregulate MAF bZIP transcription factor G (MAFG) expression in OSCC cells. Additionally, LINC00284 interacted with FUS protein to increase KAZN mRNA stability. Functional assays showed that either MAFG or KAZN overexpression promoted the malignant behaviors of OSCC cells. Through a series of rescue assays, we found that the inhibitory effect of silencing LINC00284 on OSCC cells can be reversed by upregulated MAFG and KAZN. Overall, silencing LINC00284 inhibits the malignant characteristics of OSCC cells by downregulating MAFG and inhibiting the binding of FUS to KAZN mRNA.

The clonal origin of multifocal papillary thyroid cancer: intrathyroidal spread or independent tumors?

Multifocality is a common finding in papillary thyroid cancer but the molecular pathogenesis, prognosis and management of multifocal papillary thyroid cancer are debated. The clonal origin of multifocal papillary thyroid cancer represents a controversial aspect, as two opposite viewpoints have been proposed: independent origin or intraglandular spread. Different approaches have been used for inferring the clonality of multifocal papillary thyroid cancer, including X-chromosome inactivation, mutational analysis, determination of loss of heterozygosity and, more recently, next-generation sequencing. Next-generation sequencing, able to provide information on genetic heterogeneity and phylogenetic evolution in multifocal tumors, represents the most reliable approach. While most evidences indicated an independent origin of multifocal papillary thyroid cancer, a minority of studies suggested that multifocal papillary thyroid tumors might be monoclonally derived. This discrepancy may reflect technical limitations; nevertheless, studies based on next-generation sequencing indicated that both independent and clonal origins are possible. The co-existence of multiple tumors implies a high degree of genetic heterogeneity, which may influence the best and targeted therapeutic strategy. On the other hand, intrathyroidal dissemination may indicate metastatic potential of the dominant tumor, thereby prompting more aggressive treatments. In conclusion, data available in the literature indicated that multifocal papillary thyroid cancer may derived from both intraglandular spread and independent tumor foci. The understanding of the clonal origin of multifocal papillary thyroid tumors might represent an important issue in patient treatment.

Intratumoral Genetic Heterogeneity in Papillary Thyroid Cancer: Occurrence and Clinical Significance

Intratumoral heterogeneity (ITH) refers to a subclonal genetic diversity observed within a tumor. ITH is the consequence of genetic instability and accumulation of genetic alterations, two mechanisms involved in the progression from an early tumor stage to a more aggressive cancer. While this process is widely accepted, the ITH of early stage papillary thyroid carcinoma (PTC) is debated. By different genetic analysis, several authors reported the frequent occurrence of PTCs composed of both tumor cells with and without RET/PTC or BRAF^V600E genetic alterations. While these data, and the report of discrepancies in the genetic pattern between metastases and the primary tumor, demonstrate the existence of ITH in PTC, its extension and biological significance is debated. The ITH takes on a great significance when involves oncogenes, such as RET rearrangements and BRAF^V600E as it calls into question their role of driver genes. ITH is also predicted to play a major clinical role as it could have a significant impact on prognosis and on the response to targeted therapy. In this review, we analyzed several data indicating that ITH is not a marginal event, occurring in PTC at any step of development, and suggesting the existence of unknown genetic or epigenetic alterations that still need to be identified.

Molecular Heterogeneity of Papillary Thyroid Cancer: Comparison of Primary Tumors and Synchronous Metastases in Regional Lymph Nodes by Mass Spectrometry Imaging

Intra-tumor heterogeneity results from both genetic heterogeneity of cancer (sub)clones and phenotypic plasticity of cancer cells that could be induced by different local microenvironments. Here, we used mass spectrometry imaging (MSI) to compare molecular profiles of primary tumors located in the thyroid gland and their synchronous metastases in regional lymph nodes to analyze phenotypic heterogeneity in papillary thyroid cancer. Two types of cancerous (primary tumor and metastasis) and two types of not cancerous (thyroid gland and lymph node) regions of interest (ROIs) were delineated in postoperative material from 11 patients, then the distribution of tryptic peptides (spectral components) was analyzed by MSI in all tissue regions. Moreover, tryptic peptides identified by shotgun proteomics in corresponding tissue lysates were matched to components detected by MSI to enable their hypothetical protein annotation. Unsupervised segmentation of all cancer ROIs revealed that different clusters dominated in tumor ROIs and metastasis ROIs. The intra-patient similarity between thyroid and tumor ROIs was higher than the intra-patient similarity between tumor and metastasis ROIs. Moreover, the similarity between tumor and its metastasis from the same patients was lower than similarities among tumors and among metastases from different patients (inter-patient similarity was higher for metastasis ROIs than for tumor ROIs). Components differentiating between tumor and its metastases were annotated as proteins involved in the organization of the cytoskeleton and chromatin, as well as proteins involved in immunity-related functions. We concluded that phenotypical heterogeneity between primary tumor and lymph node metastases from the same patient was higher than inter-tumor heterogeneity between primary tumors from different patients.

CHARACTERISTICS OF SUBCLONAL STRUCTURE IN THYROCYTE POPULATION IN RADIOIODINE-REFRACTORY METASTASES OF PAPILLARY THYROID CANCER

The aim of the study was cytological and immunocytochemical researches of thyrocyte populations in fine-needle aspiration smears of radioiodine-refractory metastases and their comparison with radioiodine-avid metastases and corresponding primary papillary carcinoma of the thyroid. Materials and Methods. The cytomorphological and immunocytochemical researches were conducted on the fine needle aspiration smears of 60 papillary thyroid carcinomas and 104 metastases, which were detected in the postoperative period. We applied the indirect immunoperoxidase technique using primary monoclonal mouse antibodies against leukocyte-common antigen, macrophage antigen, thyroglobulin, epithelial cell adhesion molecule, cytokeratines 7.8, polyclonal rabbit antibodies against calcitonin. Results. It was demonstrated, that radioiodine-avid metastases and corresponding primary papillary thyroid carcinoma smears had first type of cellular population with a relatively regular location of thyrocytes. Unlike them, radioiodine-refractory metastases smears had the second type of cellular population with irregularly location of thyrocytes among which showed up two cellular phenotypes. In our investigated smears some special cellular complexes were found – in 21 % of radioiodine-refractory metastases, 1 % in radioiodine-avid metastases and none of it in corresponding primary papillary thyroid. The cytological sign of cystic degeneration was found in 58 % of radioiodine-refractory metastases, but in radioiodine-avid metastases – was absent. Conclusion. The radioiodine-refractory metastases of papillary thyroid cancer demonstrated their distinction from radioiodine-uptake metastases with a presence of phenotypic heterogeneity. It is shown, that an appearance of certain cell subpopulations, special cellular complexes and cystic degeneration in fine-needle aspiration smears of radioiodine-refractory metastases, which in radioiodine-uptake metastases and corresponding primary papillary thyroid carcinomas were not found, can be used during the preoperative period to forecast the impossibility of radioiodine treatment.

New candidate genes associated to endometriosis

A previous GWAS study performed on Brazilian pooled samples indicated some SNPs (single nucleotide polymorphisms) differentially frequent in infertile patients with endometriosis and controls. Some of them were located in the genes whose biological function suggests that they could be associated with endometriosis pathogenesis; thus, the purpose here was to confirm GWAS findings in a larger group of cases and controls in order to associate the results with the pathogenesis of endometriosis. Then, a genetic association study comprising 394 infertile women with endometriosis and 650 fertile control women was conducted. TaqMan allelic discrimination assays were used to investigate the frequency of three SNPs in the genes KAZN (rs10928050), LAMA5 (rs2427284), and TAC3 (rs733629). The analysis revealed a significant association of KAZN rs10928050 (p = .015) and LAMA5 rs2427284 (p = .0059) SNPs with endometriosis-related infertility, while TAC3 rs733629 showed no difference between cases and controls. As a conclusion, it was possible to observe that individual genotyping of a larger sample of patients and controls confirmed the association among KAZN and LAMA5 with endometriosis-related infertility and revealed new candidate genes contributing to the condition.

Thyroid cancers of follicular origin in a genomic light: in-depth overview of common and unique molecular marker candidates

In recent years, thyroid malignances have become more prevalent, especially among women. The most common sporadic types of thyroid tumors of follicular origin include papillary, follicular and anaplastic thyroid carcinomas. Although modern diagnosis methods enable the identification of tumors of small diameter, tumor subtype differentiation, which is imperative for the correct choice of treatment, is still troublesome. This review discusses the recent advances in the field of molecular marker identification via next-generation sequencing and microarrays. The potential use of these biomarkers to distinguish among the most commonly occurring sporadic thyroid cancers is presented and compared. Geographical heterogeneity might be a differentiator, although not necessarily a limiting factor, in biomarker selection. The available data advocate for a subset of mutations common for the three subtypes as well as mutations that are unique for a particular tumor subtype. Tumor heterogeneity, a known issue occurring within solid malignancies, is also discussed where applicable. Public databases with datasets derived from high-throughput experiments are a valuable source of information that aid biomarker research in general, including the identification of molecular hallmarks of thyroid cancer.

Heterogeneity of Thyroid Cancer

There are 5 main histological types of thyroid cancers (TCs): papillary, follicular (also known as differentiated), poorly differentiated, anaplastic (the most aggressive form), and medullary TC, and only the latter arises from thyroid C cells. These different forms of TCs show significant variability, both among and within tumours. This great variation is particularly notable among the first 4 types, which all originate from thyroid follicular cells. Importantly, this heterogeneity is not limited to histopathological diversity only but is also manifested as variation in several genetic and/or epigenetic alterations, the numbers of interactions between the tumour and surrounding microenvironment, and interpatient differences, for example. All these factors contribute to the great complexity in the development of a tumour from cancer cells. In the present review, we summarise the knowledge accumulated about the heterogeneity of TCs. Further research in this direction should help to gain a better understanding of the underlying mechanisms contributing to the development and diversity of TCs, paving the way toward more effective treatment strategies.

Copy number profiles of paired primary and metastatic colorectal cancers

Liver metastasis is the major cause of death following a diagnosis of colorectal cancer (CRC). In this study, we compared the copy number profiles of paired primary and liver metastatic CRC to better understand how the genomic structure of primary CRC differs from the metastasis. Paired primary and metastatic tumors from 16 patients and their adjacent normal tissue samples were analyzed using single nucleotide polymorphism arrays. Genome-wide chromosomal copy number alterations were assessed, with particular attention to 188 genes known to be somatically altered in CRC and 24 genes that are clinically actionable in CRC. These data were analyzed with respect to the timing of primary and metastatic tissue resection and with exposure to chemotherapy. The genomic differences between the tumor and paired metastases revealed an average copy number discordance of 22.0%. The pairs of tumor samples collected prior to treatment revealed significantly higher copy number differences compared to post-therapy liver metastases (P = 0.014). Loss of heterozygosity acquired in liver metastases was significantly higher in previously treated liver metastasis samples compared to treatment naive liver metastasis samples (P = 0.003). Amplification of the clinically actionable genes ERBB2, FGFR1, PIK3CA or CDK8 was observed in the metastatic tissue of 4 patients but not in the paired primary CRC. These examples highlight the intra-patient genomic discrepancies that can occur between metastases and the primary tumors from which they arose. We propose that precision medicine strategies may therefore identify different actionable targets in metastatic tissue, compared to primary tumors, due to substantial genomic differences.

Intratumor and Intertumor Heterogeneity in Melanoma

Melanoma is a cancer that exhibits one of the most aggressive and heterogeneous features. The incidence rate escalates. A high number of clones harboring various mutations contribute to an exceptional level of intratumor heterogeneity of melanoma. It also refers to metastases which may originate from different subclones of primary lesion. Such component of the neoplasm biology is termed intertumor and intratumor heterogeneity. These levels of tumor heterogeneity hinder accurate diagnosis and effective treatment. The increasing number of research on the topic reflects the need for understanding limitation or failure of contemporary therapies. Majority of analyses concentrate on mutations in cancer-related genes. Novel high-throughput techniques reveal even higher degree of variations within a lesion. Consolidation of theories and researches indicates new routes for treatment options such as targets for immunotherapy. The demand for personalized approach in melanoma treatment requires extensive knowledge on intratumor and intertumor heterogeneity on the level of genome, transcriptome/proteome, and epigenome. Thus, achievements in exploration of melanoma variety are described in details. Particularly, the issue of tumor heterogeneity or homogeneity given BRAF mutations is discussed.

Next-generation sequencing in thyroid cancer

Next-generation sequencing (NGS) in thyroid cancer allows for simultaneous high-throughput sequencing analysis of variable genetic alterations and provides a comprehensive understanding of tumor biology. In thyroid cancer, NGS offers diagnostic improvements for fine needle aspiration (FNA) cytology of thyroid with indeterminate features. It also contributes to patient management, providing risk stratification of patients based on the risk of malignancy. Furthermore, NGS has been adopted in cancer research. It is used in molecular tumor classification, and molecular prediction of recurrence and metastasis in papillary thyroid carcinoma. This review covers previous NGS analyses in variable types of thyroid cancer, where samples including FNA cytology, fresh frozen tissue, and formalin-fixed, paraffin-embedded tissues were used. This review also focuses on the clinical and research implications of using NGS to study and treat thyroid cancer.

Molecular profiles of thyroid cancer subtypes: Classification based on features of tissue revealed by mass spectrometry imaging

Determination of the specific type of thyroid cancer is crucial for the prognosis and selection of treatment of this malignancy. However, in some cases appropriate classification is not possible based on histopathological features only, and it might be supported by molecular biomarkers. Here we aimed to characterize molecular profiles of different thyroid malignancies using mass spectrometry imaging (MSI) which enables the direct annotation of molecular features with morphological pictures of an analyzed tissue. Fifteen formalin-fixed paraffin-embedded tissue specimens corresponding to five major types of thyroid cancer were analyzed by MALDI-MSI after in-situ trypsin digestion, and the possibility of classification based on the results of unsupervised segmentation of MALDI images was tested. Novel method of semi-supervised detection of the cancer region of interest (ROI) was implemented. We found strong separation of medullary cancer from malignancies derived from thyroid epithelium, and separation of anaplastic cancer from differentiated cancers. Reliable classification of medullary and anaplastic cancers using an approach based on automated detection of cancer ROI was validated with independent samples. Moreover, extraction of spectra from tumor areas allowed the detection of molecular components that differentiated follicular cancer and two variants of papillary cancer (classical and follicular). We concluded that MALDI-MSI approach is a promising strategy in the search for biomarkers supporting classification of thyroid malignant tumors. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.

Same difference: A pilot study of cyclin D1, bcl-2, AMACR, and ALDH-1 identifies significant differences in expression between primary colon adenocarcinoma and its metastases

Tumor heterogeneity implies the possibility of significantly different expression of key pathways between primary and metastatic clones. Colon adenocarcinoma is one of the few tumors where current practice includes resection of primary and isolated organ metastases simultaneously without neoadjuvant therapy. We performed a pilot study on 28 cases of colon adenocarcinoma resected simultaneously with metastases in patients with no history of neoadjuvant therapy. We assayed matched primary and metastatic tumors from each patient with common diagnostic antibodies to Bcl-2, Cyclin D1, AMACR, and ALDH-1 by immunohistochemistry with semi-quantitative interpretation on archived formalin fixed, paraffin embedded samples. We were powered for large, consistent differences between primary and metastatic expression, and found 21 of 28 had a significant difference in expression of at least one of the four proteins, accounting for multiplicity of testing. Cyclin D1 had significantly more cases with differential metastatic:primary expression than would be expected by chance alone (p-value 0.0043), favoring higher expression in the metastatic sample. Bcl-2 and ALDH-1 had trends in this direction (p-value 0.078 each). Proportionately more cases with significant differences were identified when a liver metastasis was tested. We conclude differences in expression between metastatic and primary colon adenocarcinoma within the same patient exist, and may have therapeutic and biomarker testing consequences.