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According to our previous methylated-CpG island recovery assay (MIRA) and RNA expression array findings, the results indicated methylated status of Interferon regulatory factor 6 (IRF6) could be observed in most of renal cell carcinoma (RCC) cases (40.6%), and presented a negative correlation with gene expression, clear cell type of RCCs especially. As known that IRF6 is one of members of IRF family. It has been described might play an important role in epidermal cells, and correlated with cell proliferation and differentiation. The regulation of feedback loop between IRF6 and ΔNp63, which is known could control the mechanism of keratinocytes differentiation and palate closure, has also been noted. In addition, the tumor suppressor activity of IRF6 had been also demonstrated in squamous cell carcinoma associated with inhibition of tumor cell invasion and migration. The aim of this study is to clarify the clinical significance and role of IRF6 in RCC. We hypothesized low expression of IRF6 via DNA methylation might lead to irregular differentiation of RCC cells, and then further trigger cells proliferated out of control. In total, 105 pairs of clinical RCCs patients and eight RCC cell lines (included chromophobe type RCC98, sacomatoid type RCC52, clear cell type Caki-1, HH332, HOKN-9, RCC100, papillary type HH050 and adenocarcinoma 786-O), as well as Human Embryonic Kidney 293 cell used as control have involved in current study. Firstly, we performed real-time PCR on all cases. Secondly, 5-aza-2′deoxycytidine was treated on all type of RCC cell lines; it is a way of de-methylated DNA. Western blot detections were then to confirm whether the expression level of IRF6 restored in RCC cells. The IRF6 gene expressed levels differ from normal and RCC tissues were applied by the paired- T test, and shown by -ΔCT. Generally, the variant and lower level gene expression of the IRF6 could be observed from all different type of RCC cell lines, except RCC98 and RCC100 cells. After treated with 5-aza-2′deoxycytidine on RCC cell lines, the obvious expression of IRF6 was restored in all clear cell RCC cell lines. The mean - ΔCT of normal tissue was -8.0, and RCC tissue was -11.5, significantly IRF6 expressed levels differ from normal and tumor tissues could be noted (p = 0.013). The IRF6 gene was usually expressed lower level in RCC due to methylation. Our findings demonstrated the expression of IRF6 could be easily resorted by de-methylated in RCC cells, and it might further inhibit cell proliferation in the tumoral progression, and might consider as a prognostic marker to predict patients’ outcomes in RCC. However, the further cell viability and correlation with the clinical information should be further analyzed in the future. Citation Format: Chih-Yang Wei, Ying-Tzu Chen, See-Tong Pang, Wen-Hui Weng. A new prognostic marker: interferon regulatory factor 6 in renal cell carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3840. doi:10.1158/1538-7445.AM2015-3840

BACKGROUND. The mechanisms underlying the progression of prostate cancer to androgen-resistant cancer are still not fully understood. Here, we studied the genetic events associated with this transformation. METHODS. The androgen sensitive prostate cancer cells line LNCaP-FGC and its androgen resistant subline LNCaP-r were investigated using SKY, CGH, and cDNA microarray. RESULTS. Karyotypically, several additional chromosomal aberrations were seen in LNCaP-r as compared to the parental line. CGH also revealed unique net chromosomal alterations in LNCaP-r compared to LNCaP-FGC, including gain of 2p13-23, 2q21-32, and 13q and loss of 6p22-pter. cDNA microarray analysis identified several genes involved in DNA methylation, such as DNMT2, DNMT3a, and methyl-CpG binding domain protein 2 and 4 that were higher expressed in LNCaP-r. Interestingly, androgen responsiveness of LNCaP-r was restored after treated with DNA methyltransferase inhibitor. CONCLUSIONS. Our findings may serve as a basis for molecular dissection of the mechanisms involved in development of androgen resistant prostate cancer.

A lymph node metastatic cell line (UP-LN1) was established in vitro from a poorly-differentiated epithelial tumor, and characterized for immunobiological and molecular cytogenetic profiles. The morphology of UP-LN1 cells when grown as monolayers was unique in that, apart from typical colonies of adherent epithelial cells, many loosely attached round cell colonies emerged on and around the patches of epithelial cells. By means of immunofluorescence/flow cytometric analysis, UP-LN1 cells showed selective expression of cytokeratin markers AE1 and CK20, but expressed AE3 and CK7 poorly. The expression of CEA and CK20 but not CK7 in UP-LN1 cells was also exhibited in the tumor biopsy by immunohistochemistry, suggesting a gastrointestinal origin of this tumor. Down-regulation of HLA-class I and other surface molecules including ICAM-1, CD44s, CD44v5, CD44v6 and E-cadherin were observed, which all pointed to a progressive/invasive phenotype of the tumor. Spectral karyotyping revealed a hypertriploid (approximately 3n) chromosome content with 73-76 chromosomes, including numerical alterations and translocated derivative chromosomes. Seven different translocation chromosomes were observed, four of which involved chromosome 19. Numerical imbalances were also assessed by comparative genomic hybridization. This cell line should be useful for further studies of tumor invasion and metastatic processes because of the unusual in vitro and in vivo immunobiological and genetic characteristics observed.

Purpose: To evaluate known and suggested prognostic markers, especially insulin-like growth factor type 1 receptor (IGF-1R), in highly malignant soft tissue sarcomas (STS). Experimental Design: A cohort of 101 patients with primary STS of high malignancy grade was studied with respect to development of metastasis, local recurrence, and survival during a minimum of 5 years follow-up. All tumors were analyzed by immunohistochemistry for expression of Ki-67, p53, p27, Bcl-2, IGF-1R, and microvessel density. The traditional clinical variables size, malignancy grade (3 or 4), necrosis, mitotic frequency, infiltrative tumor growth, vascular invasion, depth, and surgical margins were also evaluated. Results: A significant association was shown between high expression of IGF-1R and favorable outcome. Among STS with positive IGF-1R immunoreactivity, cases with high expression (76-100% positive cells) had the best outcome, whereas cases with the lowest expression (1-25% positive cells) had the worst. As expected, large tumor size (>11 cm), presence of necrosis, high mitotic count, intralesional surgery, and deep location were all significantly associated with poor outcome, both in univariate and multivariate analyses. No difference in outcome was observed between cases of malignancy grade 3 versus 4, whereas the included and more objective variables necrosis and mitotic count were found to be reliable prognostic markers. Conclusion: IGF-1R expression is a common feature of highly malignant STS. Further elucidation of the role of IGF-1R and the IGF system in STS may both provide a basis for development of new prognostic tools in STS, as well as shed light on the basic mechanisms of the STS development.

Soft tissue sarcomas (STSs) arising in the abdominal cavity constitute a group of aggressive tumours, typically of very large size and with a high recurrence rate in the affected patients. While some distinct genetic etiologies have been described, the genetic background of this tumour group is not well characterised. Here we have assessed gross chromosomal alterations in a series of such tumours obtained from 26 patients. CGH alterations were found in tumours from 23 of the patients (88%), the most frequent being loss of 13q21 (46%) and gain of 17p and/or q (46%). Furthermore, mutations of C-KIT exon 11 were demonstrated in five tumours from four patients, and the two myxoid liposarcomas exhibited a translocation t(12;16)(q13;p11). From the pattern of chromosomal alterations detected, a genetic progression of events was clearly evident in the tumours. Taken together with analysis of subsequent relapses from the same patients, the common CGH alteration +12q13 was suggested to be a relatively early event in the genetic progression, similar to t(12;16)(q13;p11) and C-KIT mutations. Moreover, -1p21-22, -13q21, -14q, -Xp22, +9q34, +17p, +17q, and +20q13 would all represent relative later events. The most consistent alteration was loss of 13q, that was found to target the 13q14-21 and 13q34 regions as determined by CGH and Southern blot analyses. Loss of 13q was identified independently of +12q13 and C-KIT mutation and the patient's sex, and was observed in all common subtypes of STS, suggesting that it is a general and late event in the genetic progression. The findings provide a starting point for further dissection of the target genes involved in development of STSs in the abdominal cavity.

In this study, we characterized the chromosomal composition of an intra-abdominal soft tissue sarcoma diagnosed as a malignant fibrous histiocytoma (MFH). By applying a combination of spectral karyotyping, G-banding, and comparative genomic hybridization (CGH), this case was shown to carry large chromosome markers with material mainly from chromosomes 6 and 8. Further characterization of this unique tumor revealed high-level amplifications at the 6q21 approximately q23, 8p21 approximately pter, 8q24 approximately qter, and 12q13 approximately q21 regions. Using array CGH, these amplified regions were found to include MASL1 in 8p, as well s MDM2 and CDK4 in 12q, which have been shown to be amplified in MFH. Similarly, gains of 6q and 8q have also been seen in MFH. In conclusion, our study demonstrates the occurrence of large chromosome markers in MFH and suggests that the regions 6q21 approximately q23, 8p21 approximately pter, 8q24 approximately qter, and 12q13 approximately q21 might harbor oncogenes that could play a role in MFH's tumorigenesis. In addition, gain of 12q13 approximately q21, which is typical of well-differentiated liposarcoma, may also occur in MFH, supporting the previously suggested overlap in genetic etiologies between these two tumor types.

Based on our previous methylated-CpG island recovery assay (MIRA) combined with DNA microarray technique studies, several hypermethylated genes have been proven in renal cell carcinoma (RCC), in which NLRC5 was one of the interested genes. To our knowledge, this is the first study of NLRC5 in RCCs. NLRC5 was a member of the Nod-like receptors family proteins that contains C-terminal leucine-rich repeat (LRR) domain, nucleotide-binding NACHT domain and the CARD domain. It is commonly highly expressed in many immune related tissues, such as bone marrow, lymph node, spleen, thymus; besides, it also presented in normal tissues, such as kidney, liver and prostate. The function of NLRC5 has been widely proven in immunoactivities, it was known may negative regulated NF-κB and type I interferon signaling pathways, however, seldom to be studied in tumorigenesis neoplastic progression. Therefore, it led our attention to the expression of NLRC5 might regulate NF-κB activity, then further promoting the pathogenesis and metastatic behavior of RCC. Herein, we hypothesized that via demethylated NLRC5 might indirect inactivation of NF-κB then result in reducing the cancer cell proliferation. In this study we aimed to investigate the status of methylation and mRNA expression of NLRC5 in RCC. We performed reverse transcription PCR on six RCC cell lines, which included chromophobe type RCC98, sacomatoid type RCC52, clear cell type RCC100, and papillary type HH050 RCC cell lines were derived from Chang Gung Memorial Hospital, Taiwan; 786-O and HEK-293 were commercial available, in which 5-aza-2’deoxycytidine was treated on randomly selected cell lines RCC98, 786-O and HH050 to demethylate the DNA. Real-time PCR were than performed on 75 pairs of clinical RCCs samples (tumor tissue v.s normal tissue), the results were divided into two groups, high expression (T/N≥ 1.5) and low expression (T/N Citation Format: Ying-Tzu Chen, Wen-Hui Weng, See-Tong Pang. Nod-like receptors family member- NLRC5 as a useful prognostic marker in renal cell carcinomas. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1926. doi:10.1158/1538-7445.AM2013-1926

Cholangiocarcinoma (CCA) is an adenocarcinoma of the biliary tract, which is considered to be an incurable and rapidly lethal disease. A major problem with CCA surveillance is the lack of reliable biomarkers, therefore, still less no significant aspects of client-centered therapy in clinical treatment so far. Here, we established a 25th week thioacetamide (TAA)-induced cholangiocarcinoma rat cell line model named Chang Gung CCA (CGCCA), aim to figure out the early alterations of cytogenetics, molecular and protein expressed characteristics of CCA. Array comparative genomic hybridization (aCGH) and Spectral karyotyping (SKY), gene expression microarray and immunohistochemistry were performed on either rat CCA tissues or CGCCA cell line in this study. Our results showed complicated alterations of genetic gain or loss on different chromosomal regions could be observed. The data compared with the gene expression profile, thirty-three genes aberrations could be further identified; for example, tumor metastasis-related genes ANXA1 and CLCA3, the genes MMP7 and MMP12 are related with tumor invasion, and proliferation-related genes PKM2 and OSMR have been pinpointed; The number of chromosome ranging between 50 to 56 diplody (2n); despite the apparently high incidence of chromosomal translocation was revealed by cytogenetic analyses, ring and/or giant rod marker chromosomes were detected in almost every CGCCA cells, and the genetic materials are mainly included chromosomes 4 and 8. Herein, we concluded ANXA1, CLCA3, MMP7, MMP12, PKM2 and OSMR genes could be considered as potential biomarkers for the risk of disease. Supernumerary ring or giant rod marker chromosomes could also be considered as a characteristic may be involved in the late stage of CCA. However, the genes involved in the tumorigenesis should be further investigated the function of the genes. In order to verify the clinical significance and potentially to be as therapeutic targets in the future, to confirm onto a series of human CCA tissues are necessary. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3881. doi:10.1158/1538-7445.AM2011-3881

Hepatocellular carcinoma (HCC) is the fifth most common cancer in the world. The incidence rate is much higher in developing countries than in industrialized countries. More than 75% of HCC cases occur in the Far East and Southeast Asia. Gene HER1 was known commonly overexpressed in many cancers including HCC. Overexpression of HER1 would lead to cell proliferation, migration, metastasis, antiapoptosis and angiogenesis. Therefore, HER1 has been widely considered as a predict biomarker in clinical purpose. For other epidermal growth factor receptor (EGFR; HER) family members, for example HER2, HER3, and HER4, except the HER1 and HER2, HER3, HER4 are seldom to be studied in HCC so far. To our knowledge, the role of HER3 play a distinct behavior in the EGFR family, which required heterodimerization with other HER family members, then follow to trigger the signaling transduction and, therefore, result in tumor cell proliferation, migration, invasion, anti-apoptosis, and increase angiogenesis. The high level expression of HER3 has been observed in breast, ovarian, and lung cancer etc. Hence, HER3 protein expression in HCC using immunohistochemistry was also showed significantly related to cell proliferation activity, tumor size, intrahepatic metastasis, portal invasion and carcinoma differentiation. Accordingly, we hypothesized that not only HER1 but also HER3 may play an important role in HCC, and the structure of gene and copy number changes may need further investigated. We study the gene expression level of HER1 and HER3 in six HCC cell lines and twenty paraffin tissue samples using fluorescence in situ hybridization (FISH). Their expression level was also correlated with gene structures and/or gene copy number alterations. Our result showed that the gene expression of HER1 consistent the previous reports. Most notably, the gene HER3 presented either the different level of copy number changes or gene structure alterations in all six cell lines. For, most of the clinical samples only gene structure aberrations could be observed. In addition, both gene HER1 and HER3 were highly expressed in Tong cell line when compared to other HCC cell lines. The FISH results showed the alteration of genes structure and increased copy number of gene HER1 and HER3 in all cell lines. While the study on the clinical HCC samples revealed that the gene structural aberrations were more common than gene copy number alterations. However, further evidence from larger clinical samples is needed to clarify our current findings. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 332.

Background & aims: Recent evidence that ERBB3 is responsible for tumor resistance to EGFR or ERBB2 targeted therapies highlighted its crucial role in the oncogenic signaling of EGFR family. However, its roles in hepatocelluar carcinoma (HCC) remain unclear. Methods: Expression and phosphorylation of ERBB3 was examined in HCC tissues and cells. Gene number was determined using fluorescence in situ hybridization. Roles of EGEF, ERBB2, and neuregulin in phosphorylation of ERBB3 were evaluated via small-interference RNAs to silence their expression. The effects of ERBB3 on cell proliferation, invasion and tumorigenesis were assayed in vitro and in vivo. Results: Overexpression of ERBB3 was associated with a higher recurrence (P=0.000), and a worse prognosis (P=0.004). Gain of ERBB3 gene number was found in most HCC cells. EGFR, ERBB2, neuregulin and phosphorylated ERBB3 were detected in HCC cells. Phosphorylation of ERBB3 was induced by treatment with the conditioned media of HCC cells, while it was abolished by pre-treatment of the conditioned media with the anti-neuregulin antibodies or by silencing neuregulin expression. Phosphorylation of ERBB3 was suppressed by silencing the expression of ERBB2 but not EGFR. Induction of ERBB3 phosphorylation promoted cell proliferation, invasion and colony formation, while silencing ERBB3 expression suppressed xenograft tumor formation and growth in nude mice. Conclusions: Overexpression of ERBB3, primarily attributable to gene amplification, was associated with a poor prognosis of HCC. Aberrant activation of ERBB3, via an autocrine mechanism by dimerization with ERBB2, enhanced tumorigenesis in vitro and in vivo. The oncogenic signaling of ERBB3 can be the target for anti-HCC therapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3120.

The cytogenetic biomarkers to monitor tumor progression and treatment efficacy for renal cell carcinoma (RCC) are lacking. There are few known prognostic biomarkers that limited to tumor vascularization. In almost all sporadic clear cell RCC (ccRCC), the VHL gene in either mutated or methylated form is inactivated and often involved in cellular oxygen homeostasis. Herein, we compared different subtypes of RCC: ccRCC, chromophobe RCC (CRCC), and sarcomatoid clear cell RCC (sccRCC) in culture by using SKY and CGH. In addition, cytofluorometric analysis was performed on these tumors to give an overall immunophenotyping profile of these RCCs. By comparison of genomic characteristics of these RCC subtypes, deletion of chromosome 3p has been frequently found in sporadic ccRCC; and more complex genetic patterns of the high frequencies losses of heterozygous on chromosomes 1p, 2p, 6p, 10p, 13q, 17q, and 21q have also been documented in CRCC. However, for the sarcomatoid RCC subtype, such characteristcs have rarely been studied so far. In the current study, the genetic profile of CRCC revealed by SKY was shown: 74-84 XXXX, dic(1;11)(p21;q21)×2, −3, −4, −4, der(10)(q21.1- qter), −11, −11, −18, −18, der(19)t(5;19)(q31;q?)×2, −21, −21[21]; and SCCRCC cell line showed: 40-42, X,-Y; der(2)t(2,3)(q35;q21); −3; +7,+7; der(14)(14;17)(p11;q12); −14; −15; −10; −22 [22], the data were then further confirmed by CGH for gene copy number changes of the certain specific chromosomal regions. However, for the CRCC, except loss of chromosome 21, most of genetic aberrations were different from the previous reports. On the other hand, the genetic features of current sccRCC seemed not only similar to the characteristic of ccRCC (deletion 3p), but also the genetic changes sharing the those of familial RCC (t(2;3)(q35;q21)) and papillary RCC (gain of chromosome 7 and 17, and loss of Y) documented previously. Cytofluorometric analysis revealed that there were immunophenotypic differences between CRCC and sccRCC in that surface HLA class I expression was found total loss in sccRCC, whereas CRCC expressed HLA class I abundantly on the cell surface. Furthermore, bcl-2 and URO-7 were detected in the cytoplasm of CRCC, but not in sccRCC. On the other hand, CD54 was shown on cell surface; AE3, CD44v6, Hsp70, S100-β, URO-2, URO-5, URO-9 on cell cytoplasm only observed on sccRCC. In conclusion, gain of chromosome 7 and the region harbored the oncogene c-Met were found in sccRCC, which could be related with the expression of pY1349 HGFR/c-Met associated with a high pT stage and a high metastasis rate. Therefore, it is worth to further investigate the role of c-Met and its ligand HGF in sccRCC tumorigenesis, and may help to develop clinical therapeutic strategies in sccRCC. Moreover, the immunobiological evidences clarified the significant profile of these subtypes, the information is useful on predicting the patients prognosis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 330.

The immunobiology of sarcomatoid renal cell carcinoma (RCC) and how it has been transformed or progressed from clear cell-RCC are currently poorly understood. We analyzed a sarcomatoid renal carcinoma cell line (RCC52) derived from a primary clear cell renal carcinoma with intensive sarcomatoid differentiation, with respect to its immunophenotyping, molecular cytogenetic features and xenotransplantability. RCC52 cells grown as monolayers consisted of mostly small-sized epithelioid cells along with a small proportion of spindle/fibroblast-like cells, suggestive of growth of the sarcomatoid, but not clear cell component of the tumor. Cytofluorometric analysis revealed a phenotype of cell surface HLA-I−, E-CDH−, N-CDH−, EpCAM−, CD44+, CD54+, CD58+, URO1+ and URO10+ and cytoplasmic AE1+, E-CDH−, N-CDH+, Vimentin+, S100+ and VEGF+. Spectral karyotyping (SKY) show the chromosomal abnormalities in 22 metaphases examined to be 40-42,X,-Y[22]; der(2)t(2,3)(q35;q21)[20]; der(14)(14;17)(p11;q12)[22]; −3[11]; +7,+7[14]; −14[9]; −15[14]; −10[10]; −22[16]. Numerical imbalances were also assessed by comparative genomic hybridization, which are found to be consistent with the findings determined by banding and SKY. These results along with the documented genotype have established the identity of the RCC52 cell lines. Nude mouse xenografts resulting from RCC52 cell s.c. injection and the original tumor shared similar histopathology with mostly sarcomatoid elements with occasional clear cell areas, suggesting malignant potential of this cell line and the capability of sarcomatoid RCC cells to undergo transdifferentiation or dedifferentiation. The total HLA class I loss caused by the two distinctive mutations in the β2-microglobulin gene and loss of heterozygosity (LOH) in chromosome 15 observed recently (Cancer ImmunoI Immunother, 58:395-408, 2009) did not prevent sarcomatoid RCC52 cells from undergoing such transdifferentiation. Overall our results is of immunological (evasion of the host immunosurveillance) and pathobiological (progression/differentiation/transdifferentiation) significance, which forms the basis of further investigations with additional cell lines/ clones and tissues of clear cell-RCCs with sarcomatoid differentiation to confirm (i) loss HLA class I expression in most, if not all, sarcomatoid RCCs, and (ii) the proposed sequence of clear cell-RCC → fibroblast-like sarcomatoid RCC → epithelioid sarcomatoid RCC, which could in turn transdifferentiate into clear cell-RCC. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3348.

Background Aristolochic acid (AA) is a natural compound found in many plants of the Aristolochia genus, and these plants are widely used in traditional medicines for numerous conditions and for weight loss. Previous work has connected AA-mutagenesis to upper-tract urothelial cell carcinomas and hepatocellular carcinomas. We hypothesize that AA may also contribute to bladder cancer. Methods Here, we investigated the involvement of AA-mutagenesis in bladder cancer by sequencing bladder tumor genomes from two patients with known exposure to AA. After detecting strong mutational signatures of AA exposure in these tumors, we exome-sequenced and analyzed an additional 11 bladder tumors and analyzed publicly available somatic mutation data from a further 336 bladder tumors. Results The somatic mutations in the bladder tumors from the two patients with known AA exposure showed overwhelming AA signatures. We also detected evidence of AA exposure in 1 out of 11 bladder tumors from Singapore and in 3 out of 99 bladder tumors from China. In addition, 1 out of 194 bladder tumors from North America showed a pattern of mutations that might have resulted from exposure to an unknown mutagen with a heretofore undescribed pattern of A > T mutations. Besides the signature of AA exposure, the bladder tumors also showed the CpG > TpG and activated-APOBEC signatures, which have been previously reported in bladder cancer. Conclusions This study demonstrates the utility of inferring mutagenic exposures from somatic mutation spectra. Moreover, AA exposure in bladder cancer appears to be more pervasive in the East, where traditional herbal medicine is more widely used. More broadly, our results suggest that AA exposure is more extensive than previously thought both in terms of populations at risk and in terms of types of cancers involved. This appears to be an important public health issue that should be addressed by further investigation and by primary prevention through regulation and education. In addition to opportunities for primary prevention, knowledge of AA exposure would provide opportunities for secondary prevention in the form of intensified screening of patients with known or suspected AA exposure. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0161-3) contains supplementary material, which is available to authorized users.

To further delineate the role of chromosomal aberrations in non-medullary thyroid tumors, we performed cytogenetic analyses of established thyroid cancer cell lines and primary tumors using spectral karyotyping (SKY), G-banding and comparative genomic hybridization (CGH). Five of the primary thyroid tumors revealed an abnormal karyo-type. In a follicular thyroid carcinoma, we observed two translocations t(2;10), t(2;5) and losses of chromosomes 10p and 22. In a papillary thyroid carcinoma (PTC), a balanced translocation t(3;15) was revealed, while a case of metastatic PTC carried several clonal translocations involving ten different chromosomes. Numerical aberrations were observed in two of the five follicular adenomas analyzed, both leading to gain of chromosome 7 material. Furthermore, we cytogenetically characterized the three established thyroid cancer cell lines CGTH W-1, ARO and DRO. SKY, in combination with G-banding, revealed structural and numerical karyotypic abnormalities in all three cell lines and the breakpoint regions partly overlapped those of the primary tumors. The copy number changes detected by CGH correlated well with the karyotypic findings and demonstrated high-level amplifications in chromosomes 1, 5, 7, 8, 9, 11 and 19. The results provide evidence of chromosomal regions involved in non-medullary thyroid tumorigenesis, while further characterization of the observed translocations may lead to the identification of novel fusion oncogenes for thyroid cancer.