Allelic loss on chromosomes 2q21 and 19p 13.2 in oxyphilic thyroid tumors

Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples

Genomics has benefited from an explosion in affordable high-throughput technology for whole-genome sequencing. The regulatory and functional aspects in non-coding regions may be an important contributor to oncogenesis. Whole-genome tumor-normal paired alignments were used to examine the non-coding regions in five cancer types and two races. Both a sliding window and a binning strategy were introduced to uncover areas of higher than expected variation for additional study. We show that the majority of cancer associated mutations in 154 whole-genome sequences covering breast invasive carcinoma, colon adenocarcinoma, kidney renal papillary cell carcinoma, lung adenocarcinoma and uterine corpus endometrial carcinoma cancers and two races are found outside of the coding region (4 432 885 in non-gene regions versus 1 412 731 in gene regions). A pan-cancer analysis found significantly mutated windows (292 to 3881 in count) demonstrating that there are significant numbers of large mutated regions in the non-coding genome. The 59 significantly mutated windows were found in all studied races and cancers. These offer 16 regions ripe for additional study within 12 different chromosomes-2, 4, 5, 7, 10, 11, 16, 18, 20, 21 and X. Many of these regions were found in centromeric locations. The X chromosome had the largest set of universal windows that cluster almost exclusively in Xq11.1-an area linked to chromosomal instability and oncogenesis. Large consecutive clusters (super windows) were found (19 to 114 in count) providing further evidence that large mutated regions in the genome are influencing cancer development. We show remarkable similarity in highly mutated non-coding regions across both cancer and race.

Inherited Follicular Epithelial-Derived Thyroid Carcinomas: From Molecular Biology to Histological Correlates

Cancer derived from thyroid follicular epithelial cells is common; it represents the most common endocrine malignancy. The molecular features of sporadic tumors have been clarified in the past decade. However the incidence of familial disease has not been emphasized and is often overlooked in routine practice. A careful clinical documentation of family history or familial syndromes that can be associated with thyroid disease can help identify germline susceptibility-driven thyroid neoplasia. In this review, we summarize a large body of information about both syndromic and non-syndromic familial thyroid carcinomas. A significant number of patients with inherited non-medullary thyroid carcinomas manifest disease that appears to be sporadic disease even in some syndromic cases. The cytomorphology of the tumor(s), molecular immunohistochemistry, the findings in the non-tumorous thyroid parenchyma and other associated lesions may provide insight into the underlying syndromic disorder. However, the increasing evidence of familial predisposition to non-syndromic thyroid cancers is raising questions about the importance of genetics and epigenetics. What appears to be "sporadic" is becoming less often truly so and more often an opportunity to identify and understand novel genetic variants that underlie tumorigenesis. Pathologists must be aware of the unusual morphologic features that should prompt germline screening. Therefore, recognition of harbingers of specific germline susceptibility syndromes can assist in providing information to facilitate early detection to prevent aggressive disease.

Familial non-medullary thyroid cancer: unraveling the genetic maze

Familial non-medullary thyroid cancer (FNMTC) constitutes 3-9% of all thyroid cancers. Out of all FNMTC cases, only 5% in the syndromic form has well-studied driver germline mutations. These associated syndromes include Cowden syndrome, familial adenomatous polyposis, Gardner syndrome, Carney complex type 1, Werner syndrome and DICER1 syndrome. It is important for the clinician to recognize these phenotypes so that genetic counseling and testing can be initiated to enable surveillance for associated malignancies and genetic testing of family members. The susceptibility chromosomal loci and genes of 95% of FNMTC cases remain to be characterized. To date, 4 susceptibility genes have been identified (SRGAP1 gene (12q14), TITF-1/NKX2.1 gene (14q13), FOXE1 gene (9q22.33) and HABP2 gene (10q25.3)), out of which only the FOXE1 and the HABP2 genes have been validated by separate study groups. The causal genes located at the other 7 FNMTC-associated chromosomal loci (TCO (19q13.2), fPTC/ PRN (1q21), FTEN (8p23.1-p22), NMTC1 (2q21), MNG1 (14q32), 6q22, 8q24) have yet to be identified. Increasingly, gene regulatory mechanisms (miRNA and enhancer elements) are recognized to affect gene expression and FNMTC tumorigenesis. With newer sequencing technique, along with functional studies, there has been progress in the understanding of the genetic basis of FNMTC. In our review, we summarize the FNMTC studies to date and provide an update on the recently reported susceptibility genes including novel germline SEC23B variant in Cowden syndrome, SRGAP1 gene, FOXE1 gene and HABP2 genes in non-syndromic FNMTC.

Common fragile sites (CFS) and extremely large CFS genes are targets for human papillomavirus integrations and chromosome rearrangements in oropharyngeal squamous cell carcinoma

Common fragile sites (CFS) are chromosome regions that are prone to form gaps or breaks in response to DNA replication stress. They are often found as hotspots for sister chromatid exchanges, deletions, and amplifications in different cancers. Many of the CFS regions are found to span genes whose genomic sequence is greater than 1 Mb, some of which have been demonstrated to function as important tumor suppressors. CFS regions are also hotspots for human papillomavirus (HPV) integrations in cervical cancer. We used mate-pair sequencing to examine HPV integration events and chromosomal structural variations in 34 oropharyngeal squamous cell carcinoma (OPSCC). We used endpoint PCR and Sanger sequencing to validate each HPV integration event and found HPV integrations preferentially occurred within CFS regions similar to what is observed in cervical cancer. We also found that many of the chromosomal alterations detected also occurred at or near the cytogenetic location of CFSs. Several large genes were also found to be recurrent targets of rearrangements, independent of HPV integrations, including CSMD1 (2.1Mb), LRP1B (1.9Mb), and LARGE1 (0.7Mb). Sanger sequencing revealed that the nucleotide sequences near to identified junction sites contained repetitive and AT-rich sequences that were shown to have the potential to form stem-loop DNA secondary structures that might stall DNA replication fork progression during replication stress. This could then cause increased instability in these regions which could lead to cancer development in human cells. Our findings suggest that CFSs and some specific large genes appear to play important roles in OPSCC. © 2016 Wiley Periodicals, Inc.

Common chromosome fragile sites in human and murine epithelial cells and FHIT/FRA3B loss-induced global genome instability

Chromosomal positions of common fragile sites differ in lymphoblasts and fibroblasts, with positions dependent on the epigenetically determined density of replication origins at these loci. Because rearrangement of fragile loci and associated loss of fragile gene products are hallmarks of cancers, we aimed to map common fragile sites in epithelial cells, from which most cancers derive. Among the five most frequently activated sites in human epithelial cells were chromosome bands 2q33 and Xq22.1, which are not among top fragile sites identified in lymphoblasts or fibroblasts. FRA16D at 16q23 was among the top three fragile sites in the human epithelial cells examined, as it is in lymphoblasts and fibroblasts, while FRA3B at 3p14.2, the top fragile locus in lymphoblasts, was not fragile in most epithelial cell lines tested. Epithelial cells exhibited varying hierarchies of fragile sites; some frequent epithelial cell fragile sites are apparently not frequently altered in epithelial cancers and sites that are frequently deleted in epithelial cancers are not necessarily among the most fragile. Since we have reported that loss of expression of the FRA3B-encoded FHIT protein causes increased replication stress-induced DNA damage, we also examined the effect of FHIT-deficiency on markers of genome instability in epithelial cells. FHIT-deficient cells exhibited increases in fragile breaks and in γH2AX and 53BP1 foci in G1 phase cells, confirming in epithelial cells that the FHIT gene and encompassing FRA3B, is a "caretaker gene" necessary for maintenance of genome stability.

Familial nonmedullary thyroid carcinoma

BACKGROUND

Nonmedullary thyroid cancers (NMTC) originate from the follicular cells of the thyroid gland and account for over 90% of all thyroid cancers. About 3-10% of the NMTCs are of familial origin, and familial NMTC (FNMTC) is defined as two or more affected first-degree relatives with NMTC in the absence of other known familial syndromes.

SUMMARY

The genes involved in the pathogenesis of FNMTC are yet to be elucidated, although some recent studies identified several predisposition loci with a high degree of genetic heterogeneity. To date, several studies have evaluated the aggressive tumor characteristics associated with FNMTC with conflicting results. Several studies demonstrated that patients with FNMTC have increased rates of multifocal disease, extrathyroidal invasion, and involved lymph nodes compared with sporadic disease. It has been hypothesized that this increased aggressiveness translates into higher recurrence rates and decreased survival of patients with FNMTC.

CONCLUSION

This review highlights clinical aspects and management dilemmas as well as controversial issues in FNMTC. Management recommendations are deduced.

The biology and the genetics of Hurthle cell tumors of the thyroid

The biology and the genetics of Hürthle cell tumors are reviewed starting from the characterization and differential diagnosis of the numerous benign and malignant, neoplastic and nonneoplastic lesions of the thyroid in which Hürthle cell transformation is frequently observed. The clinicopathologic and molecular evidence obtained from the comparative study of the aforementioned conditions indicate that Hürthle cell appearance represents a phenotype that is superimposed on the genotypic and conventional histopathologic features of the tumors. Hürthle cell tumors differ from their non-Hürthle counterparts regarding the prevalence of large deletions of mitochondrial DNA (mtDNA), mutations of mtDNA genes coding for oxidative phosphorylation (OXPHOS) proteins (namely mutations of complex I subunit genes) and mutations of nuclear genes coding also for mitochondrial OXPHOS proteins. Such mitochondrial alterations lead to energy production defects in Hürthle cell tumors; the increased proliferation of mitochondria may reflect a compensatory mechanism for such defects and is associated with the overexpression of factors involved in mitochondrial biogenesis. The mitochondrial abnormalities are also thought to play a major role in the predisposition for necrosis instead of apoptosis which seems to be blocked in most Hürthle cell tumors. Finally, the results obtained in experimental models using cybrid cell lines and the data obtained from histopathologic and molecular studies of familial Hürthle cell tumors are used, together with the aforementioned genetic and epigenetic alterations, to progress in the understanding of the mechanisms through which mitochondrial abnormalities may be involved in the different steps of thyroid carcinogenesis, from tumor initiation to metastization.

Genome haploidisation with chromosome 7 retention in oncocytic follicular thyroid carcinoma

Background

Recurrent non-medullary thyroid carcinoma (NMTC) is a rare disease. We initially characterized 27 recurrent NMTC: 13 papillary thyroid cancers (PTC), 10 oncocytic follicular carcinomas (FTC-OV), and 4 non-oncocytic follicular carcinomas (FTC). A validation cohort composed of benign and malignant (both recurrent and non-recurrent) thyroid tumours was subsequently analysed (n = 20).

Methods

Data from genome-wide SNP arrays and flow cytometry were combined to determine the chromosomal dosage (allelic state) in these tumours, including mutation analysis of components of PIK3CA/AKT and MAPK pathways.

Results

All FTC-OVs showed a very distinct pattern of genomic alterations. Ten out of 10 FTC-OV cases showed near-haploidisation with or without subsequent genome endoreduplication. Near-haploidisation was seen in 5/10 as extensive chromosome-wide monosomy (allelic state [A]) with near-haploid DNA indices and retention of especially chromosome 7 (seen as a heterozygous allelic state [AB]). In the remaining 5/10 chromosomal allelic states AA with near diploid DNA indices were seen with allelic state AABB of chromosome 7, suggesting endoreduplication after preceding haploidisation. The latter was supported by the presence of both near-haploid and endoreduplicated tumour fractions in some of the cases. Results were confirmed using FISH analysis. Relatively to FTC-OV limited numbers of genomic alterations were identified in other types of recurrent NMTC studied, except for chromosome 22q which showed alterations in 6 of 13 PTCs. Only two HRAS, but no mutations of EGFR or BRAF were found in FTC-OV. The validation cohort showed two additional tumours with the distinct pattern of genomic alterations (both with oncocytic features and recurrent).

Conclusions

We demonstrate that recurrent FTC-OV is frequently characterised by genome-wide DNA haploidisation, heterozygous retention of chromosome 7, and endoreduplication of a near-haploid genome. Whether normal gene dosage on especially chromosome 7 (containing EGFR, BRAF, cMET) is crucial for FTC-OV tumour survival is an important topic for future research.

Microarrays

Data are made available at GEO (GSE31828).

Clinical significance of GRIM-19 expression in hepatocellular carcinoma

AIM: To investigate the clinical significance of expression of gene associated with retinoid-interferon-induced mortality-19 (GRIM-19) in hepatocellular carcinoma (HCC).

METHODS: The expression of GRIM-19 mRNA and protein in 40 cases of HCC tissues and matched non-cancerous tissues was detected by reverse transcription-polymerase chain reaction (RT-PCR), immunohistochemistry and Western blot. The correlation between GRIM-19 expression and clinicopathologic features of HCC was analyzed statistically.

RESULTS: The expression of GRIM-19 mRNA was significantly lower in HCC than in matched non-cancerous tissue (0.40 ± 0.31 vs 0.56 ± 0.67, P < 0.05). The positive rate of GRIM-19 protein expression in HCC was significantly lower than that in matched non-cancerous tissue (47.5% vs 80%, P < 0.05). The expression level of GRIM-19 protein was also significantly lower in HCC than in matched non-cancerous tissue (0.30 ± 0.29 vs 0.57 ± 0.10, P < 0.05). GRIM-19 expression differed significantly between patients with stages I + II disease and those with stages III+IV disease (0.57 ± 0.38 vs 0.30 ± 0.20, P < 0.05) as well as between patients with and without portal vein thrombosis (0.04 ± 0.02 vs 0.44 ± 0.32, P < 0.05). The expression of GRIM-19 was negatively correlated with serum AFP (r = -0.352, P < 0.05).

CONCLUSION: Decreased GRIM-19 expression is probably a significant event in the carcinogenesis of HCC and may be associated with tumor development, progression and invasion.

Chromosomal, epigenetic and microRNA-mediated inactivation of LRP1B, a modulator of the extracellular environment of thyroid cancer cells

The low-density lipoprotein receptor-related protein (LRP1B), encoding an endocytic LDL-family receptor, is among the 10 most significantly deleted genes across 3312 human cancer specimens. However, currently the apparently crucial role of this lipoprotein receptor in carcinogenesis is not clear. Here we show that LRP1B inactivation (by chromosomal, epigenetic and microRNA (miR)-mediated mechanisms) results in changes to the tumor environment that confer cancer cells an increased growth and invasive capacity. LRP1B displays frequent DNA copy number loss and CpG island methylation, resulting in mRNA underexpression. By using CpG island reporters methylated in vitro, we found that DNA methylation disrupts a functional binding site for the histone-acetyltransferase p300 located at intron 1. We identified and validated an miR targeting LRP1B (miR-548a-5p), which is overexpressed in cancer cell lines as a result of 8q22 DNA gains. Restoration of LRP1B impaired in vitro and in vivo tumor growth, inhibited cell invasion and led to a reduction of matrix metalloproteinase 2 in the extracellular medium. We emphasized the role of an endocytic receptor acting as a tumor suppressor by modulating the extracellular environment composition in a way that constrains the invasive behavior of the cancer cells.

Familial nonmedullary thyroid cancer: a review of the genetics

OBJECTIVE

Thyroid cancer, the commonest of endocrine malignancies, continues to increase in incidence with over 19,000 new cases diagnosed in the European Union per year. Although nonmedullary thyroid cancer (NMTC) is mostly sporadic, evidence for a familial form, which is not associated with other Mendelian cancer syndromes (e.g., familial adenomatous polyposis and Cowden's syndrome), is well documented and thought to cause more aggressive disease. Just over a decade ago, the search for a genetic susceptibility locus for familial NMTC (FNMTC) began. This review details the genetic studies conducted thus far in the search for potential genes for FNMTC.

DESIGN

An electronic PubMed search was performed from the English literature for genetics of FNMTC and genetics of familial papillary thyroid carcinoma (subdivision of FNMTC). The references from the selected papers were reviewed to identify further studies not found in the original search criteria.

MAIN OUTCOME

Six potential regions for harboring an FNMTC gene have been identified: MNG1 (14q32), TCO (19p13.2), fPTC/PRN (1q21), NMTC1 (2q21), FTEN (8p23.1-p22), and the telomere-telomerase complex. Important genes reported to have been excluded are RET, TRK, MET, APC, PTEN, and TSHR.

CONCLUSION

The genetics of FNMTC is an exciting field in medical research that has the potential to permit individualized management of thyroid cancer. Studies thus far have been on small family groups using varying criteria for the diagnosis of FNMTC. Results have been contradictory and further large-scale genetic studies utilizing emerging molecular screening tests are warranted to elucidate the underlying genetic basis of FNMTC.

Molecular features of thyroid oncocytic tumors

Thyroid oncocytic neoplasms are tumors composed of cells characterized by an aberrant increase of mitochondrial mass. They represent a subset of thyroid tumors whose classification and clinical features has been a matter of controversy for clinicians and pathologists alike. The prevalence of oncocytic tumors in the thyroid gland, the relevance of the issues debated, and the obvious cellular derangement of oncocytic cells, namely a complete deregulation of the mitochondrial mass and metabolism, have spurred many investigators to study the molecular mechanism underlying the genesis of this peculiar cancer phenotype. Their findings, which are unraveling the tumor pathobiology, are the subject of the present review.

Review Article: The Familial Counterparts of Follicular Cell—Derived Thyroid Tumors

The follicular cell—derived thyroid cancers (termed nonmedullary thyroid cancers—NMTCs) occur mostly sporadically, but intriguingly, NMTC has the highest familial risk among all cancer sites. This epidemiological observation is strengthened by the clinical occurrence of NMTC in familial aggregation (FNMTC) and by the detection of chromosomal loci in linkage with the disease phenotype. FNMTC loci have been proposed at 14q, 1q21, 19p13.2, 2q21, 8p23, 8q24, 1q21, and 6q22, but to date, no causative mutations have been linked to FNMTCs. In this review, the authors focus on the clinical, morphological, and molecular aspects that characterize familial tumors. Some morphological patterns may alert for a familial disease. FNMTCs share several of the somatic molecular changes associated with sporadic tumors. New genes affected by somatic changes have been disclosed within regions harboring FNMTC loci.

Loss of heterozygosity at 19p13.2 and 2q21 in tumours from familial clusters of non-medullary thyroid carcinoma

Linkage studies have identified susceptibility loci for familial nonmedullary thyroid cancer (FNMTC), with and without cell oxyphilia, at chromosomal regions 19p13.2 and 2q21. There are few genetic analyses of FNMTC tumours reported at the present time and the eventual gene involved was not identified yet. The aim of this study was to assess the occurrence of loss of heterozygosity (LOH) at these loci in the tumours from familial clusters of NMTC. We have analysed LOH in 14 tumours from 9 two-case familial clusters of NMTC. Using paired blood (normal) and tumour DNA samples, we have genotyped ten microsatellite and one SNP markers throughout 19p13.2 and fourteen microsatellite markers at 2q21. Overall, eight (57%) and two (14%) out of the fourteen tumours analysed exhibited LOH at 19p13.2 and 2q21, respectively. In two families (22%), LOH for the same markers was demonstrable in the tumours of the two members of the same family. In one family (11%) LOH was demonstrable at both loci analysed. In four two-case familial clusters (44%), LOH at the 19p13.2 locus was found in only one of the tumour cases analysed. Detailed haplotype analysis showed that, in two families (22%), the pattern of LOH in tumours was consistent with selective retention of the haplotype shared by affected members. In the remaining cases, it was consistent with random allelic losses. In conclusion, we report the finding of LOH at the 19p13.2 and 2q21 loci in tumours from familial clusters of NMTC, providing evidence that inactivation of putative genes in these regions, acting as tumour-suppressors, may be involved in the development of tumours in the context of FNMTC.

Familial nonmedullary thyroid carcinoma

BACKGROUND

Nonmedullary thyroid carcinomas (NMTCs) originate from the thyroid epithelial cells and, until recently, were thought to arise sporadically without an inherited genetic predisposition. However, evidence of a familial predisposition to NMTC is accumulating.

METHODS

This review addresses the strengths, weaknesses, and clinical implications of the observations indicating an inherited genetic predisposition to NMTC. These observations include epidemiologic studies, descriptions of large kindreds, and genetic analyses.

RESULTS

Familial NMTC (FNMTC) may be caused by an inherited genetic predisposition and can be divided into two groups. The first group has an increased prevalence of NMTC within a familial cancer syndrome with a preponderance of nonthyroidal tumors. In the second group the predominant neoplasm is NMTC, although other neoplasms may occur with increased frequency. These disorders are the focus of this review.

CONCLUSIONS

A family history in NMTC patients should be directed at detecting those familial tumor syndromes with a preponderance of NMTC as well as those familial tumor syndromes enriched in NMTC but with a preponderance of nonthyroidal tumors. Since the recurrence rates may be greater in FNMTC than in sporadic NMTC, careful monitoring is indicated for affected individuals. The advantages and disadvantages of screening asymptomatic members of FNMTC kindreds with thyroid ultrasound are discussed, and the final decision is deferred to the treating physicians and their patients. It is hoped that positional cloning research will identify the FNMTC susceptibility genes.

Promising molecular techniques for discriminating among follicular thyroid neoplasms

To guide the extent of thyroidectomy for indeterminate follicular neoplasm (FN), clinicians have long sought ways to differentiate follicular adenoma from carcinoma pre- or intraoperatively. Several promising molecular techniques have recently appeared including loss of heterozygosity analysis and molecular profiling microarray analysis. These new tools may also prove useful in determining prognosis, thus and allow a paradigm change in current management of the thyroid nodule.

Cloning of the genes for non-medullary thyroid cancer: Methods and advances

In last ten years, significant advances have occurred in thyroid endocrinology, as a consequence of the generalized use of molecular biology techniques. New genes involved in the development of thyroid cancer have been identified, which had a great impact on our understanding of thyroid cancer predisposition. All cancers are genetic in origin because they arise from mutations in a single somatic cell, but the genetic changes in sporadic cancers are confined to a particular tissue. In inherited cancers, a predisposing mutation is present in all somatic cells and in the germ line, which enables the transmission of risk to the next generation. Cancer genetics offers a model of how information on the genetics of inherited cancers could affect identification of individuals at increased genetic risk.

Bioinformatic tools for cancer geneticists

Early detection is essential for the control and prevention of many diseases, particularly cancer, which is the reason why the need for new disease markers with improved sensitivity and specificity continues to grow. Utilization of sophisticated bioinformatic tools enables the increased specificity and a relatively large quantity of high quality assays for any gene of interest. Understanding the molecular characteristics of diseases, such as cancer and the detection of mutations or changes in gene expression patterns that occur as a result of the disease, will bring researchers one step closer to achieving the predictive power needed for the development of new therapies, the design of clinical trials, and specific patient treatment planning. Genetic screening is one of the fastest moving areas of medical science, particularly in oncology, and as more genes are cloned, and more disease-associated mutations discovered, the workload is set to increase considerably with the utilization of bioinformatics tools used in integration and analysis of genomic, proteomic and metabolomic profiles of cancer. .