De novo mutations in the BMP signaling pathway in lambdoid craniosynostosis

Lambdoid craniosynostosis (CS) is a congenital anomaly resulting from premature fusion of the cranial suture between the parietal and occipital bones. Predominantly sporadic, it is the rarest form of CS and its genetic etiology is largely unexplored. Exome sequencing of 25 kindreds, including 18 parent-offspring trios with sporadic lambdoid CS, revealed a marked excess of damaging (predominantly missense) de novo mutations that account for ~ 40% of sporadic cases. These mutations clustered in the BMP signaling cascade (P = 1.6 × 10^-7), including mutations in genes encoding BMP receptors (ACVRL1 and ACVR2A), transcription factors (SOX11, FOXO1) and a transcriptional co-repressor (IFRD1), none of which have been implicated in other forms of CS. These missense mutations are at residues critical for substrate or target sequence recognition and many are inferred to cause genetic gain-of-function. Additionally, mutations in transcription factor NFIX were implicated in syndromic craniosynostosis affecting diverse sutures. Single cell RNA sequencing analysis of the mouse lambdoid suture identified enrichment of mutations in osteoblast precursors (P = 1.6 × 10^-6), implicating perturbations in the balance between proliferation and differentiation of osteoprogenitor cells in lambdoid CS. The results contribute to the growing knowledge of the genetics of CS, have implications for genetic counseling, and further elucidate the molecular etiology of premature suture fusion.

Circulating let-7e-5p, miR-106a-5p, miR-28-3p, and miR-542-5p as a Promising microRNA Signature for the Detection of Colorectal Cancer

Simple Summary

The detection of early-stage colorectal cancer increases the chance to prevent tumor progression and death by the disease. Colonoscopy is one sensitive screening test to detect malignant or potentially malignant lesions in the intestines. However, it has some disadvantages, including sedation requirements, increased risk of colon perforation, and bleeding. Circulating microRNAs (miRNAs) in plasma or serum from cancer patients have been investigated and described as potential diagnostic or prognostic markers. We conducted an miRNAs screening test in plasma samples from colorectal cancer patients and subjects without cancer, aiming to identify markers for the early detection of the disease. We identified and validated four miRNAs capable of distinguishing cancer from non-cancer cases. Our non-invasive diagnostic biomarkers presented high performance and are easily applicable to clinical practice.

Abstract

Colorectal cancer (CRC) is a disease with high incidence and mortality. Colonoscopy is a gold standard among tests used for CRC traceability. However, serious complications, such as colon perforation, may occur. Non-invasive diagnostic procedures are an unmet need. We aimed to identify a plasma microRNA (miRNA) signature for CRC detection. Plasma samples were obtained from subjects (n = 109) at different stages of colorectal carcinogenesis. The patients were stratified into a non-cancer (27 healthy volunteers, 17 patients with hyperplastic polyps, 24 with adenomas), and a cancer group (20 CRC and 21 metastatic CRC). miRNAs (381) were screened by TaqMan Low-Density Array. A classifier based on four differentially expressed miRNAs (miR-28-3p, let-7e-5p, miR-106a-5p, and miR-542-5p) was able to discriminate cancer versus non-cancer cases. The overexpression of these miRNAs was confirmed by RT-qPCR, and a cross-study validation step was implemented using eight data series retrieved from Gene Expression Omnibus (GEO). In addition, another external data validation using CRC surgical specimens from The Cancer Genome Atlas (TCGA) was carried out. The predictive model’s performance in the validation set was 76.5% accuracy, 59.4% sensitivity, and 86.8% specificity (area under the curve, AUC = 0.716). The employment of our model in the independent publicly available datasets confirmed a good discrimination performance in five of eight datasets (median AUC = 0.823). Applying this algorithm to the TCGA cohort, we found 99.5% accuracy, 99.7% sensitivity, and 90.9% specificity (AUC = 0.998) when the model was applied to solid colorectal tissues. Overall, we suggest a novel signature of four circulating miRNAs, i.e., miR-28-3p, let-7e-5p, miR-106a-5p, and miR-542-5p, as a predictive tool for the detection of CRC.

Inflammatory Breast Cancer: Clinical Implications of Genomic Alterations and Mutational Profiling

Simple Summary

Inflammatory breast cancer (IBC) is an aggressive disease with high mortality rates. Nowadays, there is no targeted treatment for this tumor type. Based on this context, we investigated the molecular profile of this disease by using well-established methodologies (high-resolution microarray platform, targeted next-generation sequencing, and immunohistochemistry) that have proven potential to unveil cancer biomarkers. We found alterations related to IBC aggressiveness and metastasis (gains of MDM4, losses of CHL1, and high homologous recombination deficiency scores), and worse overall survival (variants in HR and mismatch repair genes). We also compared the mutational profiling of our cases with literature data, which includes both non-IBC and IBC cases, validating our findings. Overall, we describe genetic alterations with the potential to be used as prognostic or predictive biomarkers and ultimately improve IBC patients’ care.

Abstract

Inflammatory breast cancer (IBC) is a rare and aggressive type of breast cancer whose molecular basis is poorly understood. We performed a comprehensive molecular analysis of 24 IBC biopsies naïve of treatment, using a high-resolution microarray platform and targeted next-generation sequencing (105 cancer-related genes). The genes more frequently affected by gains were MYC (75%) and MDM4 (71%), while frequent losses encompassed TP53 (71%) and RB1 (58%). Increased MYC and MDM4 protein expression levels were detected in 18 cases. These genes have been related to IBC aggressiveness, and MDM4 is a potential therapeutic target in IBC. Functional enrichment analysis revealed genes associated with inflammatory regulation and immune response. High homologous recombination (HR) deficiency scores were detected in triple-negative and metastatic IBC cases. A high telomeric allelic imbalance score was found in patients having worse overall survival (OS). The mutational profiling was compared with non-IBC (TCGA, n = 250) and IBC (n = 118) from four datasets, validating our findings. Higher frequency of TP53 and BRCA2 variants were detected compared to non-IBC, while PIKC3A showed similar frequency. Variants in mismatch repair and HR genes were associated with worse OS. Our study provided a framework for improved diagnosis and therapeutic alternatives for this aggressive tumor type.

Comprehensive germline mutation analysis and clinical profile in a large cohort of Brazilian xeroderma pigmentosum patients

BACKGROUND

Xeroderma pigmentosum (XP) patients present a high risk of developing skin cancer and other complications at an early age. This disease is characterized by mutations in the genes related to the DNA repair system.

OBJECTIVES

To describe the clinical and molecular findings in a cohort of 32 Brazilian individuals who received a clinical diagnosis of XP.

METHODS

Twenty-seven families were screened for germline variants in eight XP-related genes.

RESULTS

All patients (N = 32) were diagnosed with bi-allelic germline pathogenic or potentially pathogenic variants, including nine variants previously undescribed. The c.2251-1G>C XPC pathogenic variant, reported as the founder mutation in Comorian and Pakistani patients, was observed in 15 cases in homozygous or compound heterozygous. Seven homozygous patients for POLH/XPV variants developed their symptoms by an average age of 7.7 years. ERCC2/XPD, DDB2/XPE and ERCC5/XPG variants were found in a few patients. Aside from melanoma and non-melanoma skin tumours, a set of patients developed skin sebaceous carcinoma, leiomyosarcoma, angiosarcoma, mucoepidermoid carcinoma, gastric adenocarcinoma and serous ovarian carcinoma.

CONCLUSIONS

We reported a high frequency of XPC variants in 32 XP Brazilian patients. Nine new variants in XP-related genes, unexpected non-skin cancer lesions and an anticipation of the clinical manifestation in POLH/XPV cases were also described.

Long Non-coding RNAs Involved in Resistance to Chemotherapy in Ovarian Cancer

Ovarian cancer (OC) accounts for more than 150,000 deaths worldwide every year. Patients are often diagnosed at an advanced stage with metastatic dissemination. Although platinum- and taxane-based chemotherapies are effective treatment options, they are rarely curative and eventually, the disease will progress due to acquired resistance. Emerging evidence suggests a crucial role of long non-coding RNAs (lncRNAs) in the response to therapy in OC. Transcriptome profiling studies using high throughput approaches have identified differential expression patterns of lncRNAs associated with disease recurrence. Furthermore, several aberrantly expressed lncRNAs in resistant OC cells have been related to increased cell division, improved DNA repair, up-regulation of drug transporters or reduced susceptibility to apoptotic stimuli, supporting their involvement in acquired resistance. In this review, we will discuss the key aspects of lncRNAs associated with the development of resistance to platinum- and taxane-based chemotherapy in OC. The molecular landscape of OC will be introduced, to provide a background for understanding the role of lncRNAs in the acquisition of malignant properties. We will focus on the interplay between lncRNAs and molecular pathways affecting drug response to evaluate their impact on treatment resistance. Additionally, we will discuss the prospects of using lncRNAs as biomarkers or targets for precision medicine in OC. Although there is still plenty to learn about lncRNAs and technical challenges to be solved, the evidence of their involvement in OC and the development of acquired resistance are compelling and warrant further investigation for clinical applications.

GADD45B Transcript Is a Prognostic Marker in Papillary Thyroid Carcinoma Patients Treated With Total Thyroidectomy and Radioiodine Therapy

Currently, there is a lack of efficient recurrence prediction methods for papillary thyroid carcinoma (PTC). In this study, we enrolled 202 PTC patients submitted to total thyroidectomy and radioiodine therapy with long-term follow-up (median = 10.7 years). The patients were classified as having favorable clinical outcome (PTC-FCO, no disease in the follow-up) or recurrence (PTC-RE). Alterations in BRAF, RAS, RET, and TERT were investigated (n = 202) and the transcriptome of 48 PTC (>10 years of follow-up) samples was profiled. Although no mutation was associated with the recurrence risk, 68 genes were found as differentially expressed in PTC-RE compared to PTC-FCO. Pathway analysis highlighted a potential role of cancer-related pathways, including signal transduction and FoxO signaling. Among the eight selected genes evaluated by RT-qPCR, SLC2A4 and GADD45B showed down-expression exclusively in the PTC-FCO group compared to non-neoplastic tissues (NT). Increased expression of GADD45B was an independent marker of shorter disease-free survival [hazard ratio (HR) 2.9; 95% confidence interval (CI95) 1.2-7.0] in our cohort and with overall survival in the TCGA dataset (HR = 4.38, CI95 1.2-15.5). In conclusion, GADD45B transcript was identified as a novel prognostic marker candidate in PTC patients treated with total thyroidectomy and radioiodine therapy.

MicroRNAs involved in the HMGA2 deregulation and its co-occurrence with MED12 mutation in uterine leiomyoma

STUDY QUESTION

Can the mediator complex subunit 12 (MED12) mutation and high mobility group AT-hook 2 (HMGA2) overexpression co-occurrence be explained by the alternative mechanism of HMGA2 dysregulation in uterine leiomyomas (UL)?

SUMMARY ANSWER

The co-occurrence of MED12 mutation and HMGA2 overexpression, and a negative correlation of five validated or predicted microRNAs that target HMGA2 were reported.

WHAT IS KNOWN ALREADY

The recent stratification of UL, according to recurrent and mutually exclusive genomic alterations affecting HMGA2, MED12, fumarate hydratase (FH) and collagen type IV alpha 5-alpha 6 (COL4A5-COL4A6) pointed out the involvement of distinct molecular pathways. However, the mechanisms of regulation involving these drivers are poorly explored.

STUDY DESIGN, SIZE, DURATION

A total of 78 UL and 34 adjacent normal myometrium (NM) tissues was collected from 56 patients who underwent hysterectomies at a single institution. The patients were treated at the Department of Gynecology and Obstetrics, School of Medicine, Sao Paulo State University, Botucatu, SP, Brazil, from October 1995 to February 2004.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Gene expression profiling was evaluated from fresh frozen tissues and compared with MED12 mutations at exon 2. In addition, RT-qPCR was applied to evaluate the expression levels of HMGA2 and their predictive miRNA regulators: hsa-let-7a, miR-26a, miR-26b, mir-93 and mir-106b.

MAIN RESULTS AND THE ROLE OF CHANCE

An unsupervised hierarchical clustering analysis revealed two main clusters with one of them (26 of 42 UL) showing an enrichment of MED12 mutated cases (18 of 26 UL). Increased expression levels of HMGA2 were observed in both clusters, including cases with MED12 mutation (cluster 1:18 UL). A significant HMGA2 overexpression (P < 0.001) in UL in comparison with NM was found. Five miRNAs predicted to regulate HMGA2 were significantly downregulated (P < 0.001) and negatively correlated to HMGA2 expression levels (P < 0.05) in UL.

LIMITATIONS REASONS FOR CAUTION

An in vivo functional study was not performed to validate the microRNAs and HMGA2 interaction due to technical limitations.

WIDER IMPLICATIONS OF THE FINDINGS

HMGA2 overexpression was detected in a significant number of MED12 mutated ULs, suggesting that these alterations coexist. Furthermore, five miRNAs were described as potential regulators of HMGA2 expression in UL.

LARGE-SCALE DATA

Data available in the Gene Expression Omnibus GSE42939.

STUDY FUNDING AND COMPETING INTEREST(S)

This study was supported by grants from Fundação de Amparo a Pesquisa do Estado de São Paulo (# 2008/58835-2) and Conselho Nacional de Pesquisa (# 485032/2007-4), Brazil. The authors declared having no conflicts of interest.

Increased Levels of Genomic Instability and Mutations in Homologous Recombination Genes in Locally Advanced Rectal Carcinomas

Pre-operative 5-fluoracil-based chemoradiotherapy (nCRT) is the standard treatment for patients with locally advanced rectal cancer (LARC). Patients with pathological complete response (pCR–0% of tumor cells in the surgical specimen after nCRT) have better overall survival and lower risk of recurrence in comparison with incomplete responders (pIR). Predictive biomarkers to be used for new therapeutic strategies and capable of stratifying patients to avoid overtreatment are needed. We evaluated the genomic profiles of 33 pre-treatment LARC biopsies using SNP array and targeted-next generation sequencing (tNGS). Based on the large number of identified genomic alterations, we calculated the genomic instability index (GII) and three homologous recombination deficiency (HRD) scores, which have been reported as impaired DNA repair markers. We observed high GII in our LARC cases, which was confirmed in 165 rectal cancer cases from TCGA. Patients with pCR presented higher GII compared with pIR. Moreover, a negative correlation between GII and the fraction of tumor cells remaining after surgery was observed (ρ = –0.382, P = 0.02). High HRD scores were detected in 61% of LARC, of which 70% were incomplete responders. Using tNGS (105 cancer-related genes, 13 involved in HR and 5 in mismatch repair pathways), we identified 23% of cases with mutations in HR genes, mostly in pIR cases (86% of mutated cases). In agreement, the analysis of the TCGA dataset (N = 145) revealed 21% of tumors with mutations in HR genes. The HRD scores were shown to be predictive of better response to PARP-inhibitors and platinum-based chemotherapy in breast and ovarian cancer. Our results suggest that the same strategy could be applied in a set of LARC patients with HRD. In conclusion, we identified high genomic instability in LARC, which was related to alterations in the HR pathway, especially in pIR. These findings suggest that patients with impaired HRD would clinically benefit from PARP-inhibitors and platinum-based therapy.

Nuclear loss and cytoplasmic expression of androgen receptor in penile carcinomas: role as a driver event and as a prognosis factor

Androgen receptor (AR) is a member of the steroid and nuclear family receptor that acts as transcription factor. AR signaling plays pivotal role in the development and progression of prostate cancer. However, the role of AR in penile cancer (PeCa) is poorly explored. Our previous molecular studies unveiled frequent AR mRNA loss in PeCa, which was further predicted as a major driver alteration in this neoplasm. Herein, we assessed the AR protein expression in 59 usual PeCa tissues and 42 surrounding normal tissues (SNT) by immunohistochemistry using a tissue microarray. In a paired analysis, we found a total absence of nuclear AR expression in PeCa while 95.2% of SNT samples presented strong nuclear AR expression (P < 0.001). Interestingly, 17 of 42 PeCa presented weak or moderate cytoplasmic AR staining, contrasting with 5 of 42 SNT (P = 0.008). Increased levels of AR cytoplasmic expression were related with poor prognosis features including advanced clinical staging (P = 0.044), compromised surgical margins (P = 0.005), and pathological inguinal node status (P = 0.047). Furthermore, AR cytoplasmic expression was also related with shorter overall survival (P = 0.032). In conclusion, the frequent loss of nuclear AR protein levels suggests a potential function in PeCa development. Based on this result, the androgen deprivation therapy is not indicated for PeCa patients. In addition, the AR cytoplasmic expression found in a significant number of cases (40.5%) showed prognostic value and pathways activated by the non-genomic AR signaling may represent a promising therapeutic strategy.

Abstract 5360: Mutational profile and genomic instability according to response to therapy in rectal carcinomas

Rectal cancer (ReCa) patients with locally advanced disease present a high risk of locoregional recurrence and death by the disease. Preoperative neoadjuvant chemoradiotherapy (nCRT) and total mesorectal surgery have been used to reduce these events. However, nCRT has resulted in significant morbidity and up to 30% of patients present pathologic incomplete response (pIR) and ~20% develop distant metastasis or minimal regression to stable disease. These findings reinforce the relevance of identifying predictive markers of response to therapy. Genomic instability (GI) is one of the cancer hallmarks. Patterns of genomic alterations (gains, losses, and cnLOH) and the mutational profile have resulted in prognostic and predictive signatures in several cancer types. Targeted next-generation sequencing (105 cancer-related genes panel, including 13 genes involved in the homologous recombination-HR and, 5 in the mismatch repair-MMR pathways) was performed in 31/33 pretreatment ReCa biopsies. 33 samples were evaluated by SNP array to identify the GI index and the HR deficiency (HRD) scores (LST: large-scale transitions, tAI: telomeric allele imbalance, HRD-LOH: loss of heterozygosity). The GI index represents the fraction of the altered genome and the HRD scores (LST, tAI, HRD-LOH) are reported as markers of deficiency in DNA repair by HR pathway. We found 161 mutations in 51 genes; TP53 (84%), APC (81%) and KRAS (45%) were more frequently mutated. No survival differences were observed among the subgroups studied according to the presence of two APC mutations, KRAS, and TP53 mutations or lacking APC mutations. Overall, a high burden of genomic alterations was observed in ReCa samples. The median GI index was 0.358, much higher than those observed in breast cancer. Patients with complete pathologic response (pCR) presented higher GI index (0.475) compared to pIR (0.294). A significant difference was observed grouping responders (TRG 0+1) and nonresponders (TRG 2+3) (p = 0.043). The GI index of chromosome 12 was higher in pCR (p=0.019). Deficient mismatch repair indicates ineffectiveness of 5-FU used in the nCRT. Three tumors presented mutations in MLH3 or MSH6. An additional analysis performed in HR pathway genes revealed that 7/31 cases presented mutations. Three of these seven ReCa showed high tAI scores, indicating sensitivity to platinum-based therapy. HR-defective tumors have been associated with better platinum response rates. In addition, five cases presented PTEN loss; five, PIK3CA mutations; and one case, BRAF mutation. These alterations have been reported as promising predictors for treatment response in colorectal cancer. The involvement of HR pathway or other driver mutations in the response to therapy in rectal cancers remains unclear. Comprehensive studies in a large set of cases are required to confirm the predictive value of these alterations in rectal cancer.

Citation Format: Luisa Matos do Canto, Simon J. Larsen, Bruna E. Catin Kupper, Maria D. Ferreira de Souza Begnami, Cristovam Scapulatempo Neto, Jan Baumbach, Annabeth Høgh Petersen, Mads Malik Aagaard Jørgensen, Samuel Aguiar, Silvia R. Rogatto. Mutational profile and genomic instability according to response to therapy in rectal carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5360.

Deregulation of E-cadherin, β-catenin, APC and Caveolin-1 expression occurs in canine prostate cancer and metastatic processes

Prostate cancer is a heterogeneous disease with high levels of clinical and gene heterogeneity, consequently offering several targets for therapy. Dogs with naturally occurring prostate cancer are useful models for molecular investigations and studying new treatment efficacy. Three genes and proteins associated with the WNT pathway (β-catenin, APC and E-cadherin) and Caveolin-1 (CAV-1) were evaluated in canine pre-neoplastic proliferative inflammatory atrophy (PIA), prostate cancer and metastatic disease. The APC gene methylation status was also investigated. As in human prostate cancer, cytoplasmic and nuclear β-catenin, which are fundamental for activating the canonical WNT pathway, were found in canine prostate cancer and metastasis. Membranous E-cadherin was also lost in these lesions, allowing cellular migration to the stroma and nuclear localization of β-catenin. In contrast to human prostate tumours, no APC downregulation or hypermethylation was found in canine prostate cancer. The CAV-1 gene and protein overexpression were found in canine prostate cancer, and as in humans, the highest levels were found in Gleason scores ≥8. In conclusion, as with human prostate cancer, β-catenin and E-cadherin in the WNT pathway, as well as Caveolin-1, are molecular drivers in canine prostate cancer. These findings provide additional evidence that dogs are useful models for studying new therapeutic targets in prostate cancer.

Integrative miRNA and mRNA analysis in penile carcinomas reveals markers and pathways with potential clinical impact

Penile carcinoma (PeCa) is an important public health issue in poor and developing countries, and has only recently been explored in terms of genetic and epigenetic studies. Integrative data analysis is a powerful method for the identification of molecular drivers involved in cancer development and progression. miRNA and mRNA expression profiles followed by integrative analysis were investigated in 23 PeCa and 12 non-neoplastic penile tissues (NPT). Expression levels of eight miRNAs and 10 mRNAs were evaluated in the same set of samples used for microarray and in a validation set of cases (PeCa = 36; NPT = 27). Eighty-one miRNAs and 2,697 mRNAs were identified as differentially expressed in PeCa. Integrative data analysis revealed 255 mRNAs potentially regulated by 68 miRNAs. Using RT-qPCR, eight miRNAs and nine transcripts were confirmed as altered in PeCa. We identified that MMP1, MMP12 and PPARG and hsa-miR-31-5p, hsa-miR-224-5p, and hsa-miR-223-3p were able to distinguish tumors from NPT with high sensitivity and specificity. Higher MMP1 expression was detected as a better predictor of lymph node metastasis than the clinical-pathological data. In addition, PPARG and EGFR were highlighted as potential pathways for targeted therapy in PeCa. The analysis based on HPV positivity (7 of 23 cases) revealed five miRNA and 13 mRNA differentially expressed. Although in a limited number of cases, HPV positive PeCa presented less aggressive phenotype in comparison with negative cases. Overall, an integrative analysis using mRNA and miRNA profiles revealed markers related with tumor development and progression. Furthermore, MMP1 expression level was a predictive marker for lymph node metastasis in patients with PeCa.

Abstract 4287: HABP2 p.G534E variant in patients with family history of thyroid and breast cancer

Background. Familial Papillary Thyroid Carcinoma (PTC) has been recently associated with the HABP2 p.G534E mutation. In this study we evaluated the putative association of the HABP2 p.G534E mutation and familial history of PTC and Breast Carcinoma (BC) in the Brazilian population.

Methods. Germline mutations of twenty unrelated individuals with personal and/or family history of PTC and/or BC were identified by whole exome sequencing (WES), using Nextera Exome Enrichment kit and HiSeq200 platform (Illumina). Two cases were positive for p.G534E. Family members from both positive cases (seven from Family 1 and three from Family 2) were recruited for segregation analysis. An additional patient and three relatives (Family 3) with history of PTC and BC were included for validation. Fifty frozen PTC tumor samples and 170 healthy Brazilian individuals were also screened for the HABP2 variant. Confirmation and validation were performed by Sanger sequencing.

Results. Interestingly, Family 1 reported a consanguineous history, reflected in two homozygous cases: the proband (PTC) and his unaffected sister. Also, only one (BC) out of eight tested members was negative for p.G534E. In the Family 2, the only patient diagnosed with PTC was negative for the mutation, while three relatives were positive for the same loci. The index case (PTC) from Family 3, was wild type for HABP2 and three relatives tested were positive carriers. In PTC tumor samples the Allele Frequency (AF) was 0.04: two heterozygous and one homozygous for p.G534E. Among 170 healthy individuals, five were heterozygous for the variant, representing an AF of 0.0147. The two index patients evaluated by WES also presented interesting pathogenic variants in genes potentially associated with deregulation of the extracellular matrix organization pathway (CTSB, TNXB, COL4A3, COL16A1, COL24A1, COL5A2, NID1, LOXL2, MMP11, TRIM24 and MUSK) and DNA repair function (NBN and MSH2).

Conclusion. Our findings suggest that HABP2 is not a predisposition gene involved in familial PTC and BC.

Financial Support: FAPESP (2013/01867-8 and 2014/03983-8) and CNPq (481132/2012-0)

Note: This abstract was not presented at the meeting.

Citation Format: Maisa Pinheiro, Sandra A. Drigo, Fabio A. Marchi, Renata Tonhosolo, Sonia C. Andrade, Igor Jurisica, Luiz P. Kowalski, Maria Isabel W. Achatz, Silvia R. Rogatto. HABP2 p.G534E variant in patients with family history of thyroid and breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4287. doi:10.1158/1538-7445.AM2017-4287

Abstract B38: Tumor heterogeneity evaluation in glioblastomas using microarray of polysomal mRNAs

Glioblastoma is the most common primary brain malignancy in adults and one of the most aggressive cancers. The overall treatment outcome of this tumor type remains unsatisfactory even though advanced multimodal treatments including surgery, chemotherapy, and radiotherapy have been available for decades. The median survival of patients is typically less than 2 years. Insights into the genetic landscape of glioblastomas have been achieved by high-throughput studies and patterns of gene expression have been able to identify molecular subgroups with putative prognostic or predictive significance. However, this approach provides little information about protein expression levels, since the expression of mRNAs do not necessarily reflect the levels of proteins. In addition, the establishment of molecular subgroups is compounded by the endemic problem of tumor heterogeneity, since subtype classifiers are variably expressed across individual cells within a tumor and the impact of sampling bias has not been addressed. More importantly, the relationships between different sources of intratumoral heterogeneity—genetic, transcriptional and functional—remain obscure. Thus, to evaluate such intratumoral heterogeneity is fundamental to demonstrate potential therapeutic targets, source of tumor recurrences and potential prognostic implications. Herein, we evaluated a specific transcriptomic and translatomic signature of the glioblastoma heterogeneity at the single-patient level. We performed a sampling of 8 pieces from a single glioblastoma tumor. The samples could be histologically classified as high or low grade and total and polysomal mRNA was isolated and identified by microarray. By comparing histologically high vs low grade tumors we were able to identify 42 differentially transcribed and 138 differentially translated genes. Among the differentially translated genes validated by qPCR there are many related to proliferation, development and cancer, such as FOXC1, HOXB5, SNAI2, LOX, WISP1, ITGA11 and COL5A2. Thus, our results demonstrate that the isolation of mRNA engaged in translation can be used to identify biomarkers of tumor progression, leading to new therapeutic approaches. In addition, we reveal previously unappreciated heterogeneity in diverse regulatory programs central to glioblastoma biology, prognosis, and therapy.

Ethical approval: 1775/13. Funding support: FAPESP 2013/03315-2, 2014/15550-9

Citation Format: Fernanda C. S. Lupinacci, Hermano M. Bellato, Martin Roffe, Hellen Kuasne, Tiago G. Santos, Victor P. Andrade, Paulo Sanematsu, Jr., Vilma R. Martins, Silvia R. Rogatto, Glaucia N M Hajj. Tumor heterogeneity evaluation in glioblastomas using microarray of polysomal mRNAs. [abstract]. In: Proceedings of the AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; 2016 Oct 27-30; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2017;77(6 Suppl):Abstract nr B38.

Rare germline alterations in cancer-related genes associated with the risk of multiple primary tumor development

Multiple primary tumors (MPT) have been described in carriers of inherited cancer predisposition genes. However, the genetic etiology of a large proportion of MPT cases remains unclear. We reviewed 267 patients with hereditary cancer predisposition syndromes (HCPS) that underwent genetic counseling and selected 22 patients with MPT to perform genomic analysis (CytoScan HD Array, Affymetrix) aiming to identify new alterations related to a high risk of developing MPT. Twenty patients had a positive family history of cancer and 11 met phenotypic criteria for HCPS. Genetic testing for each of the genes associated with these syndromes revealed negative results for pathogenic mutations. Seventeen rare germline copy number variations (CNVs) covering 40 genes were identified in 11 patients, including an EPCAM/MSH2 deletion in one Lynch syndrome patient. An enrichment analysis revealed a significant number of genes (where the CNVs are mapped) associated with carcinogenesis and/or related to functions implicated with tumor development, such as proliferation and cell survival. An interaction network analysis highlighted the importance of TP53 pathway in cancer emergence. A high number of germline copy-neutral loss of heterozygosity (cnLOH) was identified in nine cases, particularly in two patients. Eighteen genes were covered by both rare CNVs and cnLOH, including 14 related to tumorigenesis and seven genes (ABCC1, KDM4C, KIAA0430, MYH11, NDE1, PIWIL2, and ULK2) specifically associated with cellular growth and proliferation. Overall, we identified 14 cases with rare CNVs and/or cnLOH that may contribute to the risk of MPT development.

KEY MESSAGE

CNVs may explain the risk of hereditary cancer syndromes in MPT patients. CNVs affecting genes related to cancer are candidates to be involved in MPT risk. EPCAM/MSH2 deletions should be investigated in patients suspected to have LS. Gene enrichment related to the TP53 network is associated with MPT development. cnLOH and CNVs contribute to the risk of MPT development.

Abstract A28: Differentially expressed microRNA profiles in pancreatic ductal and ampullary adenocarcinomas

Background: Pancreatic cancer is associated with 6.9% and 4% of all cancer-related deaths in the United States and Brazil, respectively. Pancreatic ductal carcinoma comprises 90% of cases, the majority being of adenocarcinoma subtype. Approximately 12% of periampullary tumors are adenocarcinomas of Vater papilla (ampullary adenocarcinomas); ampullary tumors are often associated with a better prognosis than ductal adenocarcinomas. Although genetic alterations were previously identified in pancreatic carcinomas, there is still a lack of effective treatment strategies. Therefore, the identification of new biomarkers, such as alterations in non-coding RNAs, is urgently needed for the development of novel molecularly targeted therapies for these cancers. microRNAs (miRNAs) are frequently deregulated and contribute to cancer development and progression and have potential prognostic and predictive value. Global miRNA expression profiling analysis in pancreatic cancer, followed by the identification of miRNA target genes may lead to the identification of clinically applicable biomarkers. The novel aspect of our work is the investigation of pancreatic tumors from Brazilian patients, with the inclusion of ampullary adenocarcinomas, a rare subtype.

Objectives: To identify global miRNA expression profiles and miRNA target genes in pancreatic ductal and ampullary adenocarcinomas compared to paired histologically normal pancreatic tissue.

Patients and Methods: 30 formalin fixed, paraffin embedded (FFPE) pancreatic carcinoma samples were used, including 24 pancreatic ductal adenocarcinomas (PDAC) and 6 ampullary adenocarcinomas (AMP). Paired histologically normal pancreatic tissues were used as controls. All tumor and normal tissues were needle microdissected (Leica EZ4 stereomicroscope). Global miRNA expression profiles were determined using the TaqMan Array Human MicroRNA Cards (TLDA) (card A, v3.0) (Life Technologies) platform. Data analysis was performed using the ExpressionSuite Software v1.0.3. Statistical analysis was performed to correlate miRNA expression with relevant clinical data, using SAS 9.3 software. Computational bioinformatics analysis was performed to identify miRNA target genes, as well as to construct protein-protein interaction and miRNA-gene targets networks.

Results and Discussion: We identified 63 significantly deregulated (FC≥2 and p&lt;0.05) miRNAs in PDAC (33 over- and 30 under-expressed) compared to paired histologically normal pancreatic tissue. In AMP, a group of 7 miRNAs was significantly deregulated (4 over- and 3 under-expressed) compared to normal pancreas. Our results showed differentially expressed miRNAs and a complexity of miRNA changes potentially associated to PDAC and AMP tumorigenesis. 3/7 miRNAs (miR-222, 148a and 375) were commonly deregulated in PDAC and AMP tumors. Furthermore, miRNA-gene targets networks were distinct in these different histological subtypes of pancreatic carcinomas. Global miRNA expression profiles showed that PDAC have a significantly higher number of altered miRNAs and a higher number of predicted miRNA target genes than AMP tumors, which could be potentially associated to disease progression and tumor aggressiveness in PDAC compared to AMP. Although these tumors have biological differences, commonly deregulated miRNAs in PDAC and AMP suggest that PDAC and AMP tumorigenesis may share commonly deregulated pathways.

Conclusion: miRNAs identified herein may be associated to the biology of PDAC and AMP. Among the miRNAs exclusively deregulated in PDAC, we identified known and not previously reported (novel) miRNAs. In addition, we identified several miRNA target genes associated with tumor invasion, metastasis and poor patient prognosis. Functional in vitro and in vivo validation studies may elucidate the role of identified miRNAs as modulators of oncogenesis mechanisms in PDAC and AMP.

T. Felix was funded through São Paulo Research Foundation (FAPESP), MSc. fellowship (2014/00367-4)

Citation Format: Tainara F. Felix, Tomas Tokar, Maria A. M. Rodrigues, Rogerio A. Oliveira, Claudia N. Hasimoto, Juan C. Llanos, Robson F. Carvalho, Silvia R. Rogatto, Wan Lam, Igor Jurisica, Sandra A. Drigo, Patricia P. Reis.{Authors}. Differentially expressed microRNA profiles in pancreatic ductal and ampullary adenocarcinomas. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr A28.

Genomic copy number variation associated with clinical outcome in canine cutaneous mast cell tumors

Mast cell tumors are the most common malignant cutaneous tumors in dogs. Although there are several prognostic factors involved, the clinical and biological behavior of this type of tumor varies greatly, making the best choice of treatment challenging. Molecular techniques can be used to evaluate a large number of genes involved in the neoplastic process and aid in the selection of candidate genes related to prognostic and predicting factors. Identification of the genes associated with tumor development and progression can be performed through the analysis of numerical and structural changes in DNA isolated from tumor cells by array comparative genomic hybridization (aCGH). The aim of this study was to compare copy number variations (CNVs) in cutaneous mast cell tumors of dogs that survived less than six (ST<6) and >12months (ST>12) from the date of diagnosis. Ten animals were used: four from Group ST>12 and six from Group ST<6. Genomic DNA was extracted, and aCGH was performed using Agilent Canine Genome CGH Microarray 4×180 (ID-252 552 - Agilent, USA). Data analysis was carried out using Nexus program version 5.0 (Biodiscovery, USA). The group ST>12 presented 11±3.3 CNVs, while the ST<6 group presented 85±38.5 CNVs. Regions of loss in PTEN and FAS as well as regions of gains in MAPK3, WNT5B, FGF, FOXM1 and RAD51 were detected in mast cell tumors with shorter survival times, and thus, worst prognoses, allowing for the identification of potential candidate genes for more detailed studies.

Identification of novel biomarkers associated with poor patient outcomes in invasive breast carcinoma

Breast carcinoma (BC) corresponds to 23 % of all cancers in women, with 1.38 million new cases and 460,000 deaths worldwide annually. Despite the significant advances in the identification of molecular markers and different modalities of treatment for primary BC, the ability to predict its metastatic behavior is still limited. The purpose of this study was to identify novel molecular markers associated with distinct clinical outcomes in a Brazilian cohort of BC patients. We generated global gene expression profiles using tumor samples from 24 patients with invasive ductal BC who were followed for at least 5 years, including a group of 15 patients with favorable outcomes and another with nine patients who developed metastasis. We identified a set of 58 differentially expressed genes (p ≤ 0.01) between the two groups. The prognostic value of this metastasis signature was corroborated by its ability to stratify independent BC patient datasets according to disease-free survival and overall survival. The upregulation of B3GNT7, PPM1D, TNKS2, PHB, and GTSE1 in patients with poor outcomes was confirmed by quantitative reverse transcription polymerase chain reaction (RT-qPCR) in an independent sample of patients with BC (47 with good outcomes and eight that presented metastasis). The expression of BCL2-associated agonist of cell death (BAD) protein was determined in 1276 BC tissue samples by immunohistochemistry and was consistent with the reduced BAD mRNA expression levels in metastatic cases, as observed in the oligoarray data. These findings point to novel prognostic markers that can distinguish breast carcinomas with metastatic potential from those with favorable outcomes.

Abstract 2389: Microarray analysis of polysome-associated mRNAs from different regions of the same human glioblastoma reveals intratumoral heterogeneity

Glioblastoma is among the most aggressive tumor type and less responsive to chemotherapeutic agents, thus a better understanding of the behavior of these tumors may help to develop new treatments for this disease. Currently, many genome-wide projects attempt to define general patterns of gene expression based on deep sequencing or microarray data from total mRNA populations. However, this approach provides little information about the molecular mediators of tumor biology, because the expression levels of mRNAs do not necessarily reflect the levels of proteins. The identification of mRNAs target of translational alterations in tumors can show gene expression profiles that better reflect the population of proteins. In this work we were able to identify mRNAs differentially translated in a human glioblastoma that presented histologically different parts. The sample was divided in 8 pieces that were classified as high or low grade based on histological characteristics. Actively translating ribosomes and their associated mRNAs were isolated biochemically through a polysomal profile. Total and polysomal mRNA was then extracted and submitted to a microarray analysis. By comparing high vs low grade tumor pieces, we were able to identify more differentially translated genes (138 genes) than differentially expressed genes (43 genes). Among the differentially translated mRNAs, there are many related to proliferation, development and cancer. By Integrated Pathway Analysis, we identified the TGF-β pathway among the the most relevant for grade progression. Thus, the technique of isolating mRNAs engaged in translation can be used to identify biomarkers of tumor progression, leading to new therapeutic approaches.

Citation Format: Glaucia N. Hajj, Fernanda S. Lupinacci, Martín Roffé, Hellen Kuasne, Tiago G. Santos, Victor P. Andrade, Paulo Sanematsu, Vilma R. Martins, Silvia R. Rogatto. Microarray analysis of polysome-associated mRNAs from different regions of the same human glioblastoma reveals intratumoral heterogeneity. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2389.

ROBO1 deletion as a novel germline alteration in breast and colorectal cancer patients

Despite one third of breast (BC) and colorectal cancer (CRC) cases having a hereditary component, only a small proportion can be explained by germline mutations. The aim of this study was to identify potential genomic alterations related to cancer predisposition. Copy number variations (CNVs) were interrogated in 113 unrelated cases fulfilling the criteria for hereditary BC/CRC and presenting non-pathogenic mutations in BRCA1, BRCA2, MLH1, MSH2, TP53, and CHEK2 genes. An identical germline deep intronic deletion of ROBO1 was identified in three index patients using two microarray platforms (Agilent 4x180K and Affymetrix CytoScan HD). The ROBO1 deletion was confirmed by quantitative PCR (qPCR). Six relatives were also evaluated by CytoScan HD Array. Genomic analysis confirmed a co-segregation of the ROBO1 deletion with the occurrence of cancer in two families. Direct sequencing revealed no pathogenic ROBO1 point mutations. Transcriptomic analysis (HTA 2.0, Affymetrix) in two breast carcinomas from a single patient revealed ROBO1 down-expression with no splicing events near the intronic deletion. Deeper in silico analysis showed several enhancer regions and a histone methylation mark in the deleted region. The ROBO1 deletion in a putative transcriptional regulatory region, its down-expression in tumor samples, and the results of the co-segregation analysis revealing the presence of the alteration in affected individuals suggest a pathogenic effect of the ROBO1 in cancer predisposition.

Contribution of rare germline copy number variations and common susceptibility loci in Lynch syndrome patients negative for mutations in the mismatch repair genes

In colorectal carcinoma (CRC), 35% of cases are known to have a hereditary component, while a lower proportion (∼ 5%) can be explained by known genetic factors. In this study, copy number variations (CNVs) were evaluated in 45 unrelated patients with clinical hypothesis of Lynch syndrome (Amsterdam or Bethesda criteria); negative for MLH1, MSH2, MSH6, PMS2, CHEK2*1100delC and TP53 pathogenic mutations; aiming to reveal new predisposing genes. Analyses with two different microarray platforms (Agilent 180K and Affymetrix CytoScan HD) revealed 35 rare CNVs covering 67 known genes in 22 patients. Gains (GALNT6 and GALNT11) and losses (SEMA3C) involving the same gene families related to CRC susceptibility were found among the rare CNVs. Segregation analysis performed on four relatives from one family suggested the involvement of GALNT11 and KMT2C in those at risk of developing CRC. Notably, in silico molecular analysis revealed that 61% (41/67) of the genes covered by rare CNVs were associated with cancer, mainly colorectal (17 genes). Ten common SNPs, previously associated with CRC, were genotyped in 39 index patients and 100 sporadic CRC cases. Although no significant, an increased number of risk alleles was detected in the index cases compared with the sporadic CRC patients. None of the SNPs were covered by CNVs, suggesting an independent effect of each alteration in cancer susceptibility. In conclusion, rare germline CNVs and common SNPs may contribute to an increased risk for hereditary CRC in patients with mismatch repair proficiency.

Abstract 3828: Genomic, transcriptome and epigenomic analysis reveal new genetic pathways in penile carcinoma

Background: Penile carcinoma (PeCa) is a rare and high morbidity disease. In contrast with other urological neoplasia, there is a paucity of molecular and epigenetic data in PeCa. By using integrative genetic, epigenetic and transcriptome analysis the main aim was to identify molecular drivers in PeCa.

Patients and Methods: 37 PeCa samples, 16 surrounding normal tissues and 14 normal glands were used for evaluate DNA methylation status (244K Human DNA Methylation Microarray platform, Agilent Technologies), large-scale expression (4×44K Whole Human Genome Microarray, Agilent Technologies and GeneChip® Human Transcriptome Array 2.0, Affymetrix), miRNA expression (TaqMan Human MicroRNA Array v2.0, Applied Biosystems) and genomic copy number alterations by array-CGH (Agilent Human 4×44K CGH Microarrays, Agilent Technologies). Quantitative bisulfite pyrosequencing (qBP), qPCR and RT-qPCR were used to validate the findings in an independent set of samples. HPV status was assessed using the Linear Array HPV Genotyping kit (Roche Molecular Diagnostics, CA, USA). IPA (Ingenuity Pathways Analysis) and KOBAS software were used for network analysis.

Results: HPV positivity was detected in 32% of cases, mainly for HPV16 subtype. Gain of 8q (66% of cases), where MYC gene (8q24) is mapped, was de main alteration detected by array-CGH. Gene expression profiles from both Agilent and Affymetrix microarrays identified overexpression of matrix metalloprotease and keratin gene families in tumor samples. Integrative analysis between methylome and transcriptome revealed a panel of 70 genes with inverse correlation between methylation and gene expression. Genes reported in stem cell regulation (SOX family and WNT pathway genes) were altered, suggesting the involvement of stem cells in a subset of PeCa. Concurrent CpG hypermetlylation and down-expression was confirmed in 30 genes/miRNAs. Transcriptome, methylome and miRNA profiles distinguished PeCa cases according to HPV status. Particularly, down-regulation of hsa-miR-29 family members was confirmed in HPV-positive tumors.

Conclusion: These findings suggest that deregulation of pathways related to transcriptional regulation of stem cells, matrix metalloprotease, MYC amplification and hsa-miR-29 family disruption are involved in penile carcinogenesis.

Financial support: FAPESP (2013/03667-6) and CNPq

Citation Format: Hellen Kuasne, Fabio A. Marchi, Ariane F. Busso, Mateus C. Barros-Filho, Juan JAM Muñoz, Hector Hernandez-Vargas, Cristovam Scapulatempo-Neto, Eliney F. Faria, Ademar Lopes, Gustavo C. Guimarães, Jose C. Trindade-Filho, Zdenko Herceg, Silvia R. Rogatto. Genomic, transcriptome and epigenomic analysis reveal new genetic pathways in penile 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 3828. doi:10.1158/1538-7445.AM2015-3828

Abstract 3248: Establishment and characterization of primary penile carcinoma cell culture versus xenograft by using transcriptome analysis

Background: The establishment of tumor cell lines in penile carcinoma (PeCa), a rare and high morbidity disease, is essential to conduct functional genomic and epigenomic studies. However, penile cancer cell line is not commercially available. In addition, xenograft in immunodeficient mouse is a valuable model between in vitro testing and pre-clinical trials.

Aim: This study aimed to establish and characterize PeCa primary cultures and xenografts by using large-scale gene expression analysis.

Methods: Primary tumor cultures were established from one untreated verrucous PeCa sample (HPV- negative). Tumor tissue was minced and digested with 0.2% trypsin for 30 minutes at 37°C. After extensively washing with 3 KSFM (GIBCO):1 DF12 (GIBCO). After passage 5 (36 days), two cell cultures with distinct morphologies were isolated and implanted subcutaneously on the right (epithelial cells) and left (fibroblast-like cells) flanks of BALB/C nude mouse. Analyses of AE1AE3(ABCAM), Vimentin (ABCAM), Desmin (DAKO), Myogenine (SIGMA), HHF35 (DAKO), 1A3 (SIGMA), 34βE12 (ABCAM) and CD44 (DAKO) by immunohistochemistry and ALDH (ABCAM) by flow cytometry were performed in xenograft tissues. Total RNA was extracted from cell cultures and xenograft tissues in duplicate and evaluated for gene expression by using Human Transciptome Array (HTA) 2.0 (Affymetrix). Expression Console (Affymetrix), SAM, hierarchical clustering analysis, Ingenuity Pathway Analysis (IPA).

Results: After 5 passages of verrucous PeCa cells, distinct epithelial and fibroblast-like cell morphologies were observed. After four weeks of inoculation of both cell types into right and left flanks of nude mouse, tumor growth was observed in both flanks. Both tumor tissues obtained from the patient and xenograft showed positive immunostaining for epithelial cell markers (AE1AE3, 5-10% of cells and high molecular weight cytokeratin 34βE12, 15% of cells), for mesenchymal cells (vimentin, 95%; myogenin, 95%; desmin, 80-90%; HHF35, 10%; 1A4, 95%) and also for stem cells (CD44, 5% of cells). ALDH activity was evaluated by flow cytometry and high ALDH activity was detected in vitro and in vivo cells. Preliminary results from transcriptome analysis showed 485 differentially expressed genes between primary tumor and Pre Xenograft passage 1; 502 genes in primary tumor and Pre Xenograft passage 5; 468 genes in verrucous PeCa sample vs xenografts passage 1 and 2; 402 genes in verrucous PeCa sample vs xenograft passage 3. It was verified upregulation of STAT3, IFNg, KRT14 and IFNA2 genes as well as genes involved in ROCK2 signaling networks.

Conclusions: We successfully established a primary tumor cell culture and xenograft derived from a verrucous penile carcinoma. Our data also support that despite cell cultures showed different morphologies compared to primary tumor, they present genotypic and phenotypic features similar to the tissue of origin.

Citation Format: Juan José Augusto Moyano Muñoz, Sandra A. Drigo, Tiago Goss, Hellen Kuasne, Fabio Marchi, Gustavo Guimaraes, Ademar Lopes, Cristovam S. Neto, Silvia R. Rogatto. Establishment and characterization of primary penile carcinoma cell culture versus xenograft by using transcriptome analysis. [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 3248. doi:10.1158/1538-7445.AM2015-3248

DNA methylation patterns of candidate genes regulated by thymine DNA glycosylase in patients with TP53 germline mutations

Li-Fraumeni syndrome (LFS) is a rare, autosomal dominant, hereditary cancer predisposition disorder. In Brazil, the p.R337H TP53 founder mutation causes the variant form of LFS, Li-Fraumeni-like syndrome. The occurrence of cancer and age of disease onset are known to vary, even in patients carrying the same mutation, and several mechanisms such as genetic and epigenetic alterations may be involved in this variability. However, the extent of involvement of such events has not been clarified. It is well established that p53 regulates several pathways, including the thymine DNA glycosylase (TDG) pathway, which regulates the DNA methylation of several genes. This study aimed to identify the DNA methylation pattern of genes potentially related to the TDG pathway (CDKN2A, FOXA1, HOXD8, OCT4, SOX2, and SOX17) in 30 patients with germline TP53 mutations, 10 patients with wild-type TP53, and 10 healthy individuals. We also evaluated TDG expression in patients with adrenocortical tumors (ADR) with and without the p.R337H TP53 mutation. Gene methylation patterns of peripheral blood DNA samples assessed by pyrosequencing revealed no significant differences between the three groups. However, increased TDG expression was observed by quantitative reverse transcription PCR in p.R337H carriers with ADR. Considering the rarity of this phenotype and the relevance of these findings, further studies using a larger sample set are necessary to confirm our results.

Genomic profile of a Li-Fraumeni-like syndrome patient with a 45,X/46,XX karyotype, presenting neither mutations in TP53 nor clinical stigmata of Turner syndrome

Li-Fraumeni syndrome (LFS) is a hereditary disorder that predisposes patients to several types of cancer and is associated with TP53 germline mutations. Turner syndrome (TS) is one of the most common aneuploidies in women. Patients with TS have a higher risk of developing cancer, although multiple malignant tumors are extremely rare. Herein, we describe a patient with a 45,X/46,XX karyotype with no classic phenotype of TS. She presented with a clinical diagnosis of Li-Fraumeni-like syndrome (LFL), showing papillary thyroid carcinoma and fibrosarcoma of the left flank, and had no TP53 germline mutations. Genome-wide analysis of copy number variations (CNVs) was assessed in DNA from peripheral blood cells and saliva. A total of 109 rare CNVs in the blood cells, including mosaic loss of the X chromosome (76% of cells), were identified. In saliva, three rare CNVs were detected, all of them were also detected in the blood cells: loss of 8q24.11 (EXT1), gain of 16q24.3 (PRDM7 and GAS8), and the mosaic loss of the X chromosome (50% of cells). Results of conventional G-banding confirmed the 45,X/46,XX karyotype. Surprisingly, the patient presented with an apparently normal phenotype. The PRDM and GAS8 genes are potential candidates to be associated with the risk of developing cancer in this LFL/TS patient.

Genomic profiling of human penile carcinoma predicts worse prognosis and survival

The molecular mechanisms underlying penile carcinoma are still poorly understood, and the detection of genetic markers would be of great benefit for these patients. In this study, we assessed the genomic profile aiming at identifying potential prognostic biomarkers in penile carcinoma. Globally, 46 penile carcinoma samples were considered to evaluate DNA copy-number alterations via array comparative genomic hybridization (aCGH) combined with human papillomavirus (HPV) genotyping. Specific genes were investigated by using qPCR, FISH, and RT-qPCR. Genomic alterations mapped at 3p and 8p were related to worse prognostic features, including advanced T and clinical stage, recurrence and death from the disease. Losses of 3p21.1-p14.3 and gains of 3q25.31-q29 were associated with reduced cancer-specific and disease-free survival. Genomic alterations detected for chromosome 3 (LAMP3, PPARG, TNFSF10 genes) and 8 (DLC1) were evaluated by qPCR. DLC1 and PPARG losses were associated with poor prognosis characteristics. Losses of DLC1 were an independent risk factor for recurrence on multivariate analysis. The gene-expression analysis showed downexpression of DLC1 and PPARG and overexpression of LAMP3 and TNFSF10 genes. Chromosome Y losses and MYC gene (8q24) gains were confirmed by FISH. HPV infection was detected in 34.8% of the samples, and 19 differential genomic regions were obtained related to viral status. At first time, we described recurrent copy-number alterations and its potential prognostic value in penile carcinomas. We also showed a specific genomic profile according to HPV infection, supporting the hypothesis that penile tumors present distinct etiologies according to virus status.

Down-Regulation of SLC8A1 as a Putative Apoptosis Evasion Mechanism by Modulation of Calcium Levels in Penile Carcinoma

PURPOSE

The SLC8A1 gene, which encodes the Na(+)/Ca(2+) exchanger, has a key role in calcium homeostasis. Our previous gene expression oligoarray data revealed SLC8A1 under expression in penile carcinoma. We investigated whether dysregulation of SLC8A1 expression is associated with apoptosis and cell proliferation in penile carcinoma via modulation of the calcium concentration. The underlying mechanisms of SLC8A1 under expression were also explored, focusing on copy number alteration and miRNA.

MATERIALS AND METHODS

Transcript levels of the SLC8A1 gene and miR-223 were evaluated by quantitative polymerase chain reaction to compare penile carcinoma samples with normal glans tissue. SLC8A1 copy number was evaluated by microarray based comparative genomic hybridization. In normal and tumor samples we investigated caspase-3 and Ki-67 immunostaining as well as calcium distribution by laser ablation imaging inductively coupled plasma mass spectrometry.

RESULTS

SLC8A1 under expression was detected in penile carcinoma samples (p = 0.001), confirming our previous data. It was not associated with gene copy number loss. In contrast, miR-223 over expression (p = 0.002) inversely correlated with its putative repressor SLC8A1 (r = -0.426, p = 0.015). SLC8A1 under expression was associated with decreased calcium distribution, high Ki-67 and low caspase-3 immunoexpression in penile carcinoma compared to normal tissue.

CONCLUSIONS

Down-regulation of the SLC8A1 gene, most likely mediated by its regulator miR-223, can lead to decreased calcium in penile carcinoma and consequently to suppressed apoptosis and increased tumor cell proliferation. These data suggest that the miR-223-NCX1-calcium signaling axis may represent a potential therapeutic approach to penile carcinoma.

ROCK1 as a novel prognostic marker in vulvar cancer

Background

Vulvar carcinoma is an infrequent tumour, accounting for fewer than 3% of all malignant tumours that affect women, but its incidence is rising in the past few decades. In young women, the manifestation of the vulvar carcinoma is often linked to risk factors such as smoking and HPV infection, but most cases develop in women aged over 50 years through poorly understood genetic mechanisms. Rho-associated coiled-coil-containing protein kinase 1 (ROCK1) has been implicated in many cellular processes, but its function in vulvar cancer has never been examined. In this study, we aimed to determine the prognostic value of ROCK1 gene and protein analysis in vulvar squamous cell carcinoma (VSCC).

Methods

ROCK1 expression levels were measured in 16 vulvar tumour samples and adjacent normal tissue by qRT-PCR. Further, 96 VSCC samples were examined by immunohistochemistry (IHC) to confirm the involvement of ROCK1 in the disease. The molecular and pathological results were correlated with the clinical data of the patients. Sixteen fresh VSCC samples were analyzed by array-based comparative genomic hybridization (aCGH).

Results

In each pair of samples, ROCK1 levels were higher by qRT-PCR in normal tissue compared with the tumour samples (p = 0.016). By IHC, 100% of invasive front areas of the tumour and 95.8% of central tumour areas were positive for ROCK1. Greater expression of ROCK1 was associated with the absence of lymph node metastasis (p = 0.022) and a lower depth of invasion (p = 0.002). In addition, higher ROCK1 levels correlated with greater recurrence-free survival (p = 0.001). Loss of ROCK1 was independently linked to worse cancer-specific survival (p = 0.0054) by multivariate analysis. This finding was validated by IHC, which demonstrated enhanced protein expression in normal versus tumour tissue (p < 0.001). By aCGH, 42.9% of samples showed a gain in copy number of the ROCK1 gene.

Conclusions

ROCK1 is lower expressed in tumour tissue when compared with adjacent normal vulvar epithelia. In an independent sample set of VSCCs, lower expression levels of ROCK1 correlated with worse survival rates and a poor prognosis. These findings provide important information for the clinical management of vulvar cancer.

Abstract 2242: Comprehensive genome methylation and whole genome expression analysis in penile carcinoma: Uncovering new molecular markers

Background: Penile carcinoma (PeCa) is frequently associated with high morbidity rates. Unlikely of the vast majority of tumors, there is no molecular markers described that are able to assist in diagnosis and prognosis or with potential to be therapeutic targets in PeCa.

Patients and methods: DNA methylation status (244K Human DNA Methylation Microarray platform, Agilent Technologies) and large-scale expression analysis (4x44K Whole Human Genome Microarray, Agilent Technologies) were performed in 35 and 37 PeCa, respectively. Quantitative bisulfite pyrosequencing (qBP) and RT-qPCR were used to validate the findings in 93 samples. HPV status was assessed using the Linear Array HPV Genotyping kit (Roche Molecular Diagnostics, CA, USA).

Results: Methylome analysis revealed 171 hypermethylated and 449 hypomethylated CpGs sites and the transcriptome profiling showed 2986 down- and 2817 over-expressed genes. HPV positivity was found in 32.7% of the cases, mainly the HPV16. The integrative analysis in 32 PeCa revealed a panel of 96 genes with inverse correlation between methylation and gene expression levels. The CpG hypermetlylation and gene downexpression, was confirmed for TWIST1, RSOP2, SOX3, SOX17, CD133, OTX2, HOXA3 and MEIS. In addition, BIRC5, DNMT1 and DNMT3B presented low levels of methylation and overexpression. The comparison of the results with clinical findings revealed that LIN28A, NKX2.2, NKX2.3, LHX5, BDNF, FOXA1 and CDX2 were associated with poor prognosis features.

Conclusion: Putative prognostic markers were detected revealing that DNA methylation modulates the expression of several genes in PeCa. These data may prove instrumental for biomarker discovery in clinics and molecular epidemiology of PeCa.

Citation Format: Hellen Kuasne, Ilce Mara de Syllos Colus, Hector Hernandez-Vargas, Ariane Fernanda Busso-Lopes, Mateus C. Barros-Filho, Fabio A. Marchi, Christovan Scapulatempo-Neto, Eliney F. Faria, Ademar Lopes, Gustavo C. Guimaraes, Zdenko Herceg, Silvia R. Rogatto. Comprehensive genome methylation and whole genome expression analysis in penile carcinoma: Uncovering new molecular markers. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2242. doi:10.1158/1538-7445.AM2014-2242

Abstract 4303: Bioimaging of multiple elements by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) in penile carcinomas

Background: Penile cancer (PeCa) is a rare disease associated with a high mortality and morbidity rate. Surgery is usually the clinical procedure used for the local control of this disease, which results in the partial or complete amputation of the organ and consequently in the causation of psychosexual morbidities. The imbalance of trace elements has been shown to contribute to several cancer related mechanisms, including cell proliferation, tumor progression and apoptosis. The laser ablation imaging-ICP-MS (LA(i)-ICP-MS) is a high sensitive method used as a new tool to detect trace elements associated with human cancer.

Aim: The main aim of our study is to develop a biometal imaging technique to map the spatial distribution of selected metals in cryosections of PeCa tissues in comparison to the ones in adjacent non-neoplastic and normal penile tissues.

Methods: Fresh frozen specimens of PeCa (n=3), paired adjacent non-neoplastic tissue (n=1) and normal penile tissues (obtained from autopsy; n=2) were selected and evaluated using LA-ICP-MS, for the identification of the selected trace elements: 23Na, 44Ca, 43Ca, 39K, 24Mg, 31P and 13C (reference element). The instrumental parameters of the method were optimized for the quantification of plasma energy and optimal reaction cell conditions. Experimental parameters were optimized for the speed ablation (µm s-1) and laser beam diameter (mm), energy (mJ) and frequency (Hz).

Results: The tissues were ablated using a spot size of 55µm and a scan speed of 60 µm s-1, which proved to be efficient laser parameters. The mapping of the trace elements revealed both decreased and increased levels of the different traces analyzed in the PeCa tumor cells when compared to the adjacent non-neoplastic and normal penile tissues. The same pattern of elements distribution and counts was observed in the three PeCa specimens analyzed. A lower average of element counts (43Ca/13C ratio=0.085; 44Ca/13C ratio=1.63; 23Na/13C ratio=188.91) was detected in the PeCa tissue when compared to the normal tissues (43Ca/13C ratio=0.48; 44Ca/13C ratio=6.7; 23Na/13C ratio= 336.2). In addition, PeCa presented considerably higher average counts of 24Mg, 39K and 31P (24Mg/13C ratio=18.56; 39K/13C ratio=189.12; 31P/13C ratio=18.27) compared to the normal tissues (24Mg/13C ratio=8.15; 39K/13C ratio=13.23; 31P/13C ratio=4.54).

Conclusions: LA-ICP-MS mapping is a powerful and useful method to provide novel information regarding the spatial distribution of elements in penile tumors and their implication in tumorigenesis.

Note: This abstract was not presented at the meeting.

Citation Format: Juan José Augusto Moyano Muñoz, Sandra A. Drigo, Fabio Marchi, Gustavo Pessoa, Cristovam S. Neto, Gustavo Guimaraes, Marco A Z Arruda, Silvia R. Rogatto. Bioimaging of multiple elements by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) in penile carcinomas. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4303. doi:10.1158/1538-7445.AM2014-4303

Abstract 3427: Uncovering vulvar cancer: Integrated analysis of genomic and transcriptomic data

Vulvar squamous cell carcinoma (VSCC) is a rare gynecological cancer, representing approximately 3-5% of genital tumors. However, its incidence has risen considerably and no consistent profile of this disease was established so far. Also, little is known about the genomic abnormalities of VSCC and how they correlate with gene expression. In order to verify which are the major genomic alterations that lead to gene expression abnormalities we used integrative analysis in VSCC samples. Seventeen frozen samples of VSCC were carried out in genome-wide expression (GWE) profiling using the Agilent Whole Human Genome Microarray 60K (Agilent Technologies, Santa Clara, CA, USA) and in Array-CGH (aCGH) using the Agilent Human Genome CGH Microarray 60K (Agilent Technologies, Santa Clara, CA, USA) following the manufacturer's protocol. Data were extracted and flagged with Feature Extraction version 10.5 (Agilent Technologies, Santa Clara, CA) and the aCGH data was processed using NEXUS 6.0 (BioDiscovery, Hawthorne, CA, USA). JISTIC was used to classify genes mapped at gains and losses in genomic regions. Differentially expressed genes were identified by SAM statistical test. The CONEXIC algorithm was applied to integrate the data and in silico functional analysis were performed using Ingenuity Pathways Analysis (IPA) (Ingenuity® Systems). The aCGH analysis revealed 216 significant genomic alterations including 196 gains and 20 losses. GWE profile identified 3799 differentially expressed genes in comparison with normal tissue including 1352 up-regulated and 2447 down-regulated. The integrated analysis showed that genomic and transcriptomic results were concordant in 47 genes, in which 46 were up regulated and involved in gain of DNA copy number and only 1 gene (PLXDC2) was down-regulated and associated to genomic loss. According to IPA analysis of the top biological functions associated with the 47 genes, 3 of them were related with “tumor morphology”. Also, “cell death and survival” and “cellular function and maintenance” were included in the list of pathways disrupted by the genes selected as possible drivers of VSCC. Three significant networks could be defined comprising these genes. The first network comprised 18 of the concordant genes and was associated to functions as carbohydrate metabolism, small molecule biochemistry, cellular function and maintenance. The second network (18 genes) was related to RNA post-transcriptional modification, developmental disorder and hereditary disorder. The third network (15 genes) was associated to RNA post-transcriptional modification, gene expression and organ development. Thereby, important signaling networks were found disrupted by these genes which could influence tumor development or progression in VSCC. Therefore, these genes might be useful as a first step to identify molecular markers to improve diagnosis and therapeutic approaches for this tumor.

Citation Format: André M. Lavorato-Rocha, Beatriz de Melo Maia, Iara S. Rodrigues, Fabio A. Marchi, Gabriel R. Fernandes, Glauco Baiocchi, Fernando A. Soares, Silvia R. Rogatto, Yukie Sato-Kuwabara, Rafael M. Rocha. Uncovering vulvar cancer: Integrated analysis of genomic and transcriptomic data. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3427. doi:10.1158/1538-7445.AM2014-3427

Gene expression profiling in leiomyosarcomas and undifferentiated pleomorphic sarcomas: SRC as a new diagnostic marker

Background

Undifferentiated Pleomorphic Sarcoma (UPS) and high-grade Leiomyosarcoma (LMS) are soft tissue tumors with an aggressive clinical behavior, frequently developing local recurrence and distant metastases. Despite several gene expression studies involving soft tissue sarcomas, the potential to identify molecular markers has been limited, mostly due to small sample size, in-group heterogeneity and absence of detailed clinical data.

Materials and Methods

Gene expression profiling was performed for 22 LMS and 22 UPS obtained from untreated patients. To assess the relevance of the gene signature, a meta-analysis was performed using five published studies. Four genes (BAD, MYOCD, SRF and SRC) selected from the gene signature, meta-analysis and functional in silico analysis were further validated by quantitative PCR. In addition, protein-protein interaction analysis was applied to validate the data. SRC protein immunolabeling was assessed in 38 UPS and 52 LMS.

Results

We identified 587 differentially expressed genes between LMS and UPS, of which 193 corroborated with other studies. Cluster analysis of the data failed to discriminate LMS from UPS, although it did reveal a distinct molecular profile for retroperitoneal LMS, which was characterized by the over-expression of smooth muscle-specific genes. Significantly higher levels of expression for BAD, SRC, SRF, and MYOCD were confirmed in LMS when compared with UPS. SRC was the most value discriminator to distinguish both sarcomas and presented the highest number of interaction in the in silico protein-protein analysis. SRC protein labeling showed high specificity and a positive predictive value therefore making it a candidate for use as a diagnostic marker in LMS.

Conclusions

Retroperitoneal LMS presented a unique gene signature. SRC is a putative diagnostic marker to differentiate LMS from UPS.

Non-hematopoietic PAR-2 is essential for matriptase-driven pre-malignant progression and potentiation of ras-mediated squamous cell carcinogenesis

The membrane-anchored serine protease, matriptase, is consistently dysregulated in a range of human carcinomas, and high matriptase activity correlates with poor prognosis. Furthermore, matriptase is unique among tumor-associated proteases in that epithelial stem cell expression of the protease suffices to induce malignant transformation. Here, we use genetic epistasis analysis to identify proteinase-activated receptor (PAR)-2-dependent inflammatory signaling as an essential component of matriptase-mediated oncogenesis. In cell-based assays, matriptase was a potent activator of PAR-2, and PAR-2 activation by matriptase caused robust induction of nuclear factor (NF)κB through Gαi. Importantly, genetic elimination of PAR-2 from mice completely prevented matriptase-induced pre-malignant progression, including inflammatory cytokine production, inflammatory cell recruitment, epidermal hyperplasia and dermal fibrosis. Selective ablation of PAR-2 from bone marrow-derived cells did not prevent matriptase-driven pre-malignant progression, indicating that matriptase activates keratinocyte stem cell PAR-2 to elicit its pro-inflammatory and pro-tumorigenic effects. When combined with previous studies, our data suggest that dual induction of PAR-2-NFκB inflammatory signaling and PI3K-Akt-mTor survival/proliferative signaling underlies the transforming potential of matriptase and may contribute to pro-tumorigenic signaling in human epithelial carcinogenesis.

ATM down-regulation is associated with poor prognosis in sporadic breast carcinomas

BACKGROUND

Ataxia telangiectasia-mutated (ATM) gene downexpression has been reported in sporadic breast carcinomas (BC); however, the prognostic value and mechanisms of ATM deregulation remain unclear.

PATIENTS AND METHODS

ATM and miRNAs (miR-26a, miR-26b, miR-203, miR-421, miR-664, miR-576-5p and miR-18a) expression levels were evaluated by quantitative real-time PCR (RT-qPCR) in 52 BC and 3 normal breast samples. ATM protein expression was assessed by immunohistochemistry in 968 BC and 35 adjacent normal breast tissues. ATM copy number alteration was detected by array comparative genomic hybridization (aCGH) in 42 tumours.

RESULTS

Low ATM levels were associated with tumour grade. Absence of ATM protein expression was associated with distant metastasis (P < 0.001), reduced disease-free survival (DFS, P < 0.001) and cancer-specific survival (CSS, P < 0.001). Multivariate analysis indicated ATM protein expression as an independent prognostic marker for DFS (P = 0.001, HR = 0.579) and CSS (P = 0.001, HR = 0.554). ATM copy number loss was detected in 12% of tumours and associated with lower mRNA levels. miR-421 over-expression was detected in 36.5% of cases which exhibit lower ATM transcript levels (P = 0.075, r = -0.249).

CONCLUSIONS

The data suggest that ATM protein expression is an independent prognostic marker in sporadic BC. Gene copy number loss and miR-421 over-expression may be involved in ATM deregulation in BC.

Alterations of C-MYC, NKX3.1, and E-cadherin expression in canine prostate carcinogenesis

The dog (canis lupus familiaris) is the only other species besides humans that develop spontaneous prostatic carcinomas (PCa) at a high frequency. The canine model is primarily utilized for the study of the PCa molecular mechanisms and provides a natural animal model for the study of potential therapies. In humans, the PCa frequently exhibits mutations in the C-MYC and a reduced expression of the E-cadherin and NKX3.1 proteins. This study's objective was to evaluate the NKX3.1, C-MYC, and E-cadherin expression in the canine normal prostate, benign prostatic hyperplasia (BPH), proliferative inflammatory atrophy (PIA) and PCa and to verify differences in expression and subcellular localization of these proteins in the prostatic carcinogenesis. A tissue microarray (TMA) slide was constructed, and immunohistochemistry with antibodies raised against C-MYC, NKX3.1, E-cadherin and p63 was performed using the peroxidase and DAB methods. The C-MYC protein expression was elevated in the cytoplasm and nuclei of the canine PCa and PIA compared with the normal prostate (P = 0.004. The NKX3.1 protein expression was reduced in 94.75% of the PCa and 100% of the PIA compared with the normal prostate (P = 0.0022). In fact, the expression of E-cadherin trended towards a decrease in carcinomas when compared to normal prostate and PIA. By immunohistochemistry, more p63-positive basal cells were observed in the PCa and PIA when compared with the normal prostate (P = 0.0002). This study has demonstrated that the carcinogenesis of canine prostatic tissue may be related to basal cell proliferation, the gain of C-MYC function and the loss of NKX3.1 protein expression.

STEAP1 protein overexpression is an independent marker for biochemical recurrence in prostate carcinoma

AIMS

To investigate the prognostic value of expression levels of the genes STEAP1 and STEAP2, and of STEAP1 protein, in prostate carcinomas (PCa).

METHODS AND RESULTS

STEAP1 and STEAP2 transcript levels were evaluated by RT-qPCR in samples from 35 PCa, 24 adjacent non-neoplastic prostate (AdjP) tissues, five cases of benign prostatic hyperplasia (BPH), and two histologically normal prostates (N). STEAP1 expression was assessed by immunohistochemistry in samples from 198 PCa, 76 AdjP, 22 BPH, and two N. The findings were compared with clinical and pathological parameters and patient outcome. STEAP1 and STEAP2 transcript analysis showed no differences between the groups tested. Although not significant, higher STEAP1 mRNA levels were detected in tumours with high Gleason scores and in patients who presented with biochemical recurrence (BCR). STEAP1 overexpression was detected in PCa, and was significantly associated with high-grade Gleason scores, seminal vesicle invasion, BCR, and worse outcome (metastasis or PCa-specific death). STEAP1 overexpression was significantly associated with shorter BCR-free survival. Multivariate analysis revealed that STEAP1 is an independent marker for BCR.

CONCLUSIONS

These findings provide evidence that STEAP1 is a biomarker of worse prognosis in PCa patients.

Abstract 1916: Integrative analysis of DNA copy number and gene expression in oropharyngeal squamous cell carcinomas

Head and neck squamous cell carcinomas (HNSCC) are the sixth prevalent cancer by incidence worldwide. The major risk factors associated with HNSCC are tobacco usage, alcohol consumption and human papillomavirus (HPV) infection. Only 40%-50% of patients survive more than three years, even with the advances in surgical techniques and the recognized benefits of chemotherapy. Integrative studies using genomic alterations and large-scale expression analysis have been used to find functionally relevant molecular drivers and targets for therapy. The aim of this study was to investigate biological markers as potential predictors of response to chemo and radiotherapy according to HPV infection in oropharyngeal carcinomas (OC). Thirty-three fresh OC biopsies were genotyped for HPV, evaluated by array CGH (4x180k, Agilent) and by gene expression large-scale analysis (4x44k, Agilent). Approximately 54% of cases were HPV positive with HPV16 (16/33) being the most frequently detected, followed by HPV 18 (1/33) and HPV 16/18 (1/33). The most frequent copy number alterations were losses on 8p11.23-p11.22, 14q11.1-q11.2, 15q11.2 and gains on 11q13.2 and 11q13.2-q13.3 (p&lt;0.05). Comparative analysis of genomic alterations according to HPV status revealed gains of 3q26.31 and 11q13.2 and losses of 9p21.3 exclusively in HPV negative cases (p&lt;0.05). Gains of 11q13.2-q13.4 were statistically associated with progressive disease. The amplicon 11q13 (where is mapped CCND1, FADD and PPFIA1) is frequently reported as involved in HNSCC. In this study this amplicon was associated with progressive disease and unfavorable prognosis. In agreement with literature, the majority of unfavorable treatment response cases were HPV negative (71.4%). These cases presented more CNAs compared to HPV positive cases. According to HPV status, it was identified 798 differentially expressed genes, 407 down- and 391 up-regulated. The integrative analysis using genomic and transcriptomic data was performed using R tools (positive correlation: R&gt;0.5 and negative: R&lt;0.5). It was identified 61 genes correlated by both procedures, 52 showed positive correlation (10/52 gain/up-regulated and 42/52 deletion/down-regulated) and 9 negative correlation (4/9 gain/down-regulated and 5/9 loss/up-regulated). Both genes mapped on 11q13, CCND1 and PPFIA1, were confirmed as associated with unfavorable response to treatment in OC, showing copy number gains and transcripts overexpression. This analysis demonstrated biological markers as potential predictors of response to chemotherapy and/or radiotherapy according to HPV infection in oropharyngeal carcinomas.

Citation Format: Marcia Hatakeyama, Luciana A. Reis-Rosa, Fabio A. Marchi, Graziela Spilborghs, André L. Carvalho, Ulisses M. Ribaldo, Luiz P. Kowalski, Silvia R. Rogatto. Integrative analysis of DNA copy number and gene expression in oropharyngeal squamous 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 1916. doi:10.1158/1538-7445.AM2013-1916

Abstract 1553: Down-expression of ATM gene and protein associated with canine breast tumors

Background: Ataxia telangiectasia mutated (ATM) gene encodes a protein associated with DNA damage repair that plays an important role in the maintenance of genome integrity. ATM transcript and protein down-regulation have been reported in sporadic breast carcinomas and the absence of ATM protein expression was also significantly associated with distant metastasis in women, but the mechanisms involved in the ATM deregulation are not well established.

Aim: Due to the fact that mammary tumor biological behavior is similar between canine and humans, we evaluate ATM gene and protein expression in canine breast cancer and compared with normal mammary gland from dogs.

Patients and methods: Fresh samples of non-metastatic (n=23) and metastatic mammary carcinomas (n=11) and normal breasts (n=10) were evaluated for ATM gene expression by RT-qPCR and from the same animals, another sample of tumor was collected, formalin-fixed and paraffin-embedded to assess ATM protein expression by immunohistochemistry. Evaluation of ATM protein expression was performed by the distribution of positively-immunostained tumor cells in scores: 1 (&lt;25% cells positive), 2 (26% to 50% cells positive) and 3 (&gt;51% cells positive).

Results: Down expression of ATM was detected in tumors samples (non-metastatic and metastatic mammary carcinomas) when compared to normal breast samples (P= 0,0414). Additionally, scores 1 and 2 of ATM protein expression were exclusively observed in metastatic tumors presenting score 1: 18% (2 out of 11), score 2: 55% (6 out to 11) and non metastatic tumors presenting the same score 1 and 2: 17% (4 out to 23) while all normal breast tissues showed score 3 (P=0,0087).

Conclusions: Down expression of ATM transcript was confirmed by ATM protein expression. Low levels of ATM suggest an involvement of DNA damage repair transcript and protein in tumorigenesis process of canine mammary tumors, as in women, corroborating for the use of dogs as a natural comparative model to study mammary gland tumors in humans.

Citation Format: Talita Mariana Morata Raposo, Renata C. Bueno, Márcio de Carvalho, Carlos E. Fonseca-Alves, Mirela Tinucci-Costa, Andrigo B. De Nardi, Silvia R. Rogatto, Renée Laufer-Amorim. Down-expression of ATM gene and protein associated with canine breast tumors. [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 1553. doi:10.1158/1538-7445.AM2013-1553

Abstract 317: Role of ATM and PTEN in prostatic carcinogenic dog prostate: validation of aCGH results

The canis lupus familiares is the only species besides human that spontaneously develop prostatic carcinoma (PCa). In addition, the metastatic sites are similar to those frequently reported in men. For these reasons, the dog is the best natural model to study the molecular mechanisms in PCa development providing a natural animal model for treatment by molecular targets. Previously, we investigated copy number alterations by arrayCGH (Canine Genome CGH Microarray 4x44K-G2519F, Agilent Technologies) in canine prostatic lesions: 3 benign prostatic hyperplasias (BPH), 4 proliferative inflammatory atrophies (PIA), and 14 PCa. Five histologically normal prostatic tissues were used as reference. Genomic alterations were evaluated using Genomic Workbench Standard Edition 5.0.14. This previous study revealed significant copy number losses of Atm and Pten exclusively in PCa. In the present study, ATM and PTEN immunoexpression were investigated using a tissue microarray (TMA) containing 149 canine prostatic paraffin-embedded lesions (BPH, PIA and PCa) collected from 67 animals. Immunohistochemical reactions were performed using the polyclonal rabbit antibody anti-PTEN (Santa Cruz Biotech, 1:50) and anti-ATM (Abcam, 1:50). The sections were developed with diaminobenzidine (DAB) and peroxidase. The immunohistochemical staining was assessed in each core by the distribution of positive cells for each antibody per lesion (score 1: &lt;25% cells positive, 2: 26% to 50%, 3: being 51% and 75% and 4:&gt; 75%) and intensity (1: weak, 2: moderate, 3: intense). Chi-square or Fisher exact test was used to determine the association between the categorical variables using GraphPad Prism 5 (GraphPad Software Inc., La Jolla, CA). Distribution of positive cells did not differ among lesions. PCa and PIA showed more samples with weak intensity for ATM when compared to normal prostatic tissue and BPH (PCa: p=0,032 and PIA: p=0,025). Benign prostatic hyperplasia and normal samples presented intense PTEN immunostaining than PCa (p=0,021) and PIA (p=0,0013). These results suggest that ATM and PTEN proteins expression in canine prostatic carcinoma are downregulated possibly by copy number losses. These findings are similar from those described in prostate carcinomas from human corroborating for the use of dogs as a natural model to study prostatic disease in men.

Citation Format: Carlos E. Fonseca Alves, Patricia R. Pellicciari, Marcela M. P. Rodrigues, Silvia R. Rogatto, Renee L. Amorim. Role of ATM and PTEN in prostatic carcinogenic dog prostate: validation of aCGH results. [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 317. doi:10.1158/1538-7445.AM2013-317

Chromogenic in situ hybridization compared with other approaches to evaluate HER2/neu status in breast carcinomas

Human epidermal growth factor receptor 2 (HER2) has been evaluated in breast cancer patients to identify those most likely to benefit from herceptin-targeted therapy. HER2 amplification, detected in 20-30% of invasive breast tumors, is associated with reduced survival and metastasis. The most frequently used technique for evaluating HER2 protein status as a routine procedure is immunohistochemistry (IHC). HER2 copy number alterations have also been evaluated by fluorescence in situ hybridization (FISH) in moderate immunoexpression (IHC 2+) cases. An alternative procedure to evaluate gene amplification is chromogenic in situ hybridization (CISH), which has some advantages over FISH, including the correlation between HER2 status and morphological features. Other methodologies have also been used, such as silver-enhanced in situ hybridization (SISH) and quantitative real-time RT-PCR, to determine the number of HER2 gene copies and expression, respectively. Here we will present a short and comprehensive review of the current advances concerning HER2 evaluation in human breast cancer.

Common chromosomal imbalances and stemness-related protein expression markers in endometriotic lesions from different anatomical sites: the potential role of stem cells

BACKGROUND

Endometriosis is a multifactorial gynecological disease characterized by the presence of functional endometrium-like tissue in ectopic sites. Several studies have focused on elucidating the immunological, endocrine, environmental and genetic factors involved in endometriosis. However, its pathogenesis is still unclear.

METHODS

High-resolution comparative genomic hybridization was applied to screen for genomic imbalances in laser microdissected stromal and epithelial cells from 20 endometriotic lesions and three samples of eutopic endometrium derived from eight patients. The expression of seven stemness-related markers (CD9, CD13, CD24, CD34, CD133, CD117/c-Kit and Oct-4) in endometrial tissue samples was evaluated by immunohistochemistry.

RESULTS

Samples of eutopic endometrium showed normal genomic profiles. In ectopic tissues, an average of 68 genomic imbalances was detected per sample. DNA losses were more frequently detected and involved mainly 3p, 5q, 7p, 9p, 11q, 16q, 18q and 19q. Many of the genomic imbalances detected were common to endometriotic stroma and epithelia and also among different endometriotic sites from the same patient. These findings suggested a clonal origin of the endometriotic cells and the putative involvement of stem cells. Positive immunostaining for CD9, CD34, c-Kit and Oct-4 markers was detected in isolated epithelial and/or stromal cells in eutopic and ectopic endometrium in the majority of cases.

CONCLUSIONS

The presence of shared genomic alterations in stromal and epithelial cells from different anatomical sites of the same patient and the expression of stemness-related markers suggested that endometriosis arises as a clonal proliferation with the putative involvement of stem cells.

Abstract 1665: High resolution genome profile in familial colorectal cases without mutations on mismatch repair genes

Colorectal cancer (CRC) represents the fourth leading cause of cancer mortality. Approximately 30% of all CRC cases have a hereditary component, but only 5% are associated with inherited mutations in known genes. The most common hereditary syndrome of CRC is the Lynch syndrome (LS) and is caused by mutations in mismatch repair genes, mainly MLH1 and MSH2. In ∼50% of families classified with the Amsterdam criteria not show germline mutations in mismatch repair genes, suggesting that other genetic factors are associated with predisposition to CRC. In this study, it was evaluated germline copy number alterations (CNAs) in 57 LS patients without pathogenic mutations in mismatch repair genes (MLH1, MSH2, MSH6, PMS1 and PMS2), as well as in CHEK2 and TP53, by array comparative genomic hybridization (aCGH) using a platform of 4x180K (Agilent). Genomic data were extracted with Feature Extraction software and analyzed using Nexus 6.0 software, statistical algorithm FASST2 Segmentation and sensitivity threshold of 5.0E-6. The aCGH data showed a total of 361 CNAs (in average, 6.3±3.8 CNA/individual) including 144 gains and 217 genomic losses. After the comparison with a reference dataset obtained from 100 healthy Brazilian individuals (Krepischi et al, 2011; personal communication) and exclusion of the CNAs detected in more than 5% of this reference dataset, it was identified ∼100 rare CNAs. Most of them were detected in only one case, however, six CNAs were common at least in five cases: 1p11.2, 1p36.32, 7p22.3, 8q24.3, 9p11.2 and 18q11.1. The ROCK1 gene, mapped on 18q11.1, was found as involved in nine cases (three losses and six gains). This gene was associated with carcinogenesis and progression of human tumors, including colon cancer (Nakashima et al, Int J Oncol. 36:585, 2010). Amplification on 7p22.3 (5 cases), where is mapped the homeobox gene UNCX, a transcription factor involved in somitogenesis and neurogenesis. Mutations in rare constitutional CNAs may affect genes or major pathways associated with cancer, offering an explanation for families with high cancer risk. In CRC, the large scale analysis of germline CNAs in patients and their relatives can allow the identification of new genes involved in tumor predisposition. Financial support: FAPESP and CNPq

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1665. doi:1538-7445.AM2012-1665