Discovery of Novel miRNAs in Colorectal Cancer: Potential Biological Roles and Clinical Utility

Deregulated miRNAs are associated with colorectal cancer (CRC), with alterations depending on the tumor location. Novel tissue-specific miRNAs have been identified in different tumors and are associated with cancer. We used miRMaster to identify novel miRNAs in CRC from the TCGA and GEO data (discovery and validation groups). We used TCGA data from five tissues to analyze miRNA tissue specificity. miRDB was used to predict miRNA targets, and the UCSC Xena Browser was used to evaluate target expression. After successive analyses, we identified 15 novel miRNAs with the same expression patterns in CRC in both the discovery and validation groups. Four molecules (nov-miR-13844-5p, nov-miR-7154-5p, nov-miR-5035-3p, and nov-miR-590-5p) were differentially expressed in proximal and distal CRC. The nov-miR-3345-5p and nov-miR-13172-3p, which are upregulated in tumors, are only expressed in colorectal tissues. These molecules have been linked to a worse prognosis in right-sided colon and rectal carcinomas. An analysis revealed an association between eight novel miRNAs and 81 targets, mostly cancer-related genes, with varying expression based on tumor location. These findings provide new miRNAs with potential biological relevance, molecular biomarkers, and therapeutic targets for CRC treatment.

Abstract 3763: microRNAs associated with metastatic potential in salivary gland mucoepidermoid carcinoma

Mucoepidermoid carcinoma (MEC) is the most common malignant tumor of the salivary glands. Metastatic spread occurs in up to 80% of high-grade tumors and it is a strong predictor of poor outcome, however, the mechanisms underlying this process are largely unknown. Large-scale microRNA expression profiling studies of human cancers have demonstrated that dysregulation of miRNA is frequently associated with many cancer types. The aim of this study was to investigate the microRNA profile in metastatic versus non-metastatic MECs. Using Real Time RT-PCR (qPCR) we have analyzed the expression of 384 miRNAs and controls in 4 non-metastatic MECs, 3 MECs with lymph node metastasis, 3 MECs with distant metastasis, and 2 non-neoplastic human salivary gland samples. The microRNA profile was able to discriminate between non-neoplastic and tumor samples and between metastatic and non-metastatic tumors. Considering non-neoplastic samples and non-metastatic MECs, 12 microRNAs were differentially expressed. The non-neoplastic versus lymph node metastasis MEC analysis demonstrated that 10 microRNAs were differentially expressed. Considering non-neoplastic versus distant metastasis MECs, 3 microRNAs were differentially expressed: 1 down-regulated and 2 up-regulated. Comparing non-metastatic MECs versus lymph node metastasis MECs we observed 17 up-regulated microRNAs. Considering non-metastatic MECs versus distant metastasis MECs, 2 microRNAs were up-regulated. One microRNA is differentially expressed between lymph node metastasis MECs and distant metastasis MECs. Our results suggest that microRNA profiles could discriminate the metastatic potential of salivary MECs and might be helpful in diagnostic and prognostic evaluation of patients.

Citation Format: Maria Eduarda S. Trevizani, Katia K. Oliveira, Fabio A. Marchi, Daniela Bizinelli, Fernanda V. Mariano, Cibele P. Nagano, Felipe A. Costa, Clóvis A. Pinto, Luiz P. Kowalski, Silvia V. Lourenço, Cláudia M. Coutinho-Camillo. microRNAs associated with metastatic potential in salivary gland mucoepidermoid carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3763.

Genomic and transcriptomic characterization of the human glioblastoma cell line AHOL1

Cancer cell lines are widely used as in vitro models of tumorigenesis, facilitating fundamental discoveries in cancer biology and translational medicine. Currently, there are few options for glioblastoma (GBM) treatment and limited in vitro models with accurate genomic and transcriptomic characterization. Here, a detailed characterization of a new GBM cell line, namely AHOL1, was conducted in order to fully characterize its molecular composition based on its karyotype, copy number alteration (CNA), and transcriptome profiling, followed by the validation of key elements associated with GBM tumorigenesis. Large numbers of CNAs and differentially expressed genes (DEGs) were identified. CNAs were distributed throughout the genome, including gains at Xq11.1-q28, Xp22.33-p11.1, Xq21.1-q21.33, 4p15.1-p14, 8q23.2-q23.3 and losses at Yq11.21-q12, Yp11.31-p11.2, and 15q11.1-q11.2 positions. Nine druggable genes were identified, including HCRTR2, ETV1, PTPRD, PRKX, STS, RPS6KA6, ZFY, USP9Y, and KDM5D. By integrating DEGs and CNAs, we identified 57 overlapping genes enriched in fourteen pathways. Altered expression of several cancer-related candidates found in the DEGs-CNA dataset was confirmed by RT-qPCR. Taken together, this first comprehensive genomic and transcriptomic landscape of AHOL1 provides unique resources for further studies and identifies several druggable targets that may be useful for therapeutics and biologic and molecular investigation of GBM.

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.

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.

Abstract B13: BLM, FOXO3, FOXK2, FOXM1, FOXR1 genes as therapeutic targets to neuroblastoma

Due to heterogeneity of the neuroblastoma (NB) tumor, next-generation personalized medicine may identify therapeutic targets. Gene expression alterations of BLM (Bloom Syndrome RecQ Like Helicase) and FOX (Forkhead-box) family have been associated with an increased risk for cancer and resistance to chemotherapy drugs. Considering the potential implication of these genes on the clinical management of NB, we correlated clinical parameters, such as survival and treatments with genetic profiles of 11 NB patients stage 3 and 4 with MYCN-amplified (4 patients) or MYCN-non-amplified (7 patients) and one patient stage 2B and MYCN-non-amplified. Patients were treated with doxorubicin, etoposide, topotecan, cyclophosphamide, vincristine, and carboplatin. Targeted DNA sequencing, methylation array, and mRNA expression were performed on tumor and blood peripheral of these patients. Multiplex ligation-dependent probe amplification (MLPA). All variants considered important were validated by Sanger sequencing. Polymorphisms were identified using dbSNP138, 1000 genomes Project Consortium and NHLBI Exome Sequencing Project (ESP) databases with minor allele frequencies recorded from each database.

In this study, we observed in a patient with 17 months, diagnosed with MYCN-non amplified (11q-,+17p,+9p) stage 3 NB, a variant in FOXO3 gene (rs201947198) and BLM gene (rs28384991) with low frequency in the population (0.001% and 1%, respectively). FOXO3 and BLM gene expressions were decreased while FOXM1 gene expression was increased. This patient received chemotherapy and 2 years after the end of therapy, NB recurred locally. Six years after the diagnosis, the patient is still alive and receives chemotherapy.

In other case, we found a patient of 13 months, diagnosed with MYCN amplified (+2p,+3p,+17q) stage 3 NB, three synonymous variants in BLM gene (rs2227933,rs2227934,rs1063147). These variants have been shown to affect protein levels and function. We also identified an important variant in FOXO3 gene (rs 111556510) with low frequency in the population. FOXM1 mutation was not found in this patient and FOXM1 RNAm was increased. This patient received chemotherapy and despite the treatment, died 6 months after the diagnosis.

As relapse with a second event, we found two variants in BLM gene (rs2227935 and rs7167216), in a patient diagnosed at 6 months, stage 2B, MYCN-non-amplified (+2p;+3p;-11q;+17) NB, who received chemotherapy but has recurred three times at the same local site, despite the treatment. These variants are polymorphism low frequency and databases of the prediction algorithms, considered the SNP p.P868L damage. The variant identified in FOXR1 gene (c.C517G:p.R173G). This variant has not been described to NB. Further, hypermethylation in the promoter region of FOXK2 was correlated with decreased FOXK2 RNAm. Many studies have shown that epigenetic silencing of FOXK2 gene increases resistance to chemotherapy drugs. Other patients (3 MYCN-amplified and 6 MYCN-non-amplified) were found only polymorphisms synonymous in the BLM gene (rs2227933, rs2227934, and rs1063147). Moreover, variants or alterations in FOXO3, FOXR1, FOXK2 expression were not found. However, FOXM1 expression was increased in these patients.

Conclusion: Many studies have shown that personalized oncology plays an important role in treatment of cancer patients. In this study, we demonstrated that variants in FOXO3, FOXR1 and BLM genes, FOXM1 expression and silencing epigenetic of FOXK2 found in 3/12 patients with refractory relapse disease may be candidate targets for personalized therapy in neuroblastoma.

Citation Format: Thamiris Magalhaes Gimenez, Nathalia Halley Neves, Andreia Rangel Santos, Fabio A. Marchi, Leslie Kulikowski, Lilian M. Cristofani, Estela M. Novak, Vicente Odone Filho. BLM, FOXO3, FOXK2, FOXM1, FOXR1 genes as therapeutic targets to neuroblastoma [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr B13.

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

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.

An Integrative Approach Uncovers Biomarkers that Associate with Clinically Relevant Disease Outcomes in Vulvar Carcinoma

Vulvar squamous cell carcinoma (VSCC) is a rare disease that has a high mortality rate (∼40%). However, little is known about its molecular signature. Therefore, an integrated genomics approach, based on comparative genome hybridization (aCGH) and genome-wide expression (GWE) array, was performed to identify driver genes in VSCC. To achieve that, DNA and RNA were extracted from frozen VSCC clinical specimens and examined by aCGH and GWE array, respectively. On the basis of the integration of data using the CONEXIC algorithm, PLXDC2 and GNB3 were validated by RT-qPCR. The expression of these genes was then analyzed by IHC in a large set of formalin-fixed paraffin-embedded specimens. These analyses identified 47 putative drivers, 46 of which were characterized by copy number gains that were concomitant with overexpression and one with a copy number loss and downregulation. Two of these genes, PLXDC2 and GNB3, were selected for further validation: PLXDC2 was downregulated and GNB3 was overexpressed compared with non-neoplastic tissue. By IHC, both proteins were ubiquitously expressed throughout vulvar tissue. High expression of GNB3 and low PLXDC2 immunostaining in the same sample was significantly associated with less lymph node metastasis and greater disease-free survival. On the basis of a robust methodology never used before for VSCC evaluation, two novel prognostic markers in vulvar cancer are identified: one with favorable prognosis (GNB3) and the other with unfavorable prognosis (PLXDC2).

IMPLICATIONS

This genomics study reveals markers that associate with prognosis and may provide guidance for better treatment in vulvar cancer. Mol Cancer Res; 14(8); 720-9. ©2016 AACR.

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 4915: Tracking genomic alterations in young patients with head and neck carcinomas using whole-exome sequencing

Head and neck squamous cell carcinomas (HNSCC) often affect patients over 60 years, although epidemiological studies have shown an increased incidence in young adults (18-45 years), especially those having oropharynx and oral cavity tumors. There is no consensus regarding the etiology, clinical course and prognosis of HNSCC in young patients that often do not have the risk factors frequently described as associated with the disease (alcohol consumption, smoking and HPV infection). Despite its importance, studies with this group of patients are scarce, mainly focusing on the molecular aspects involved in the development and progression of the disease. In this study, we evaluated 36-paired samples (6 oral cavity, 12 oropharyngeal carcinomas and 18 matched blood samples) by whole exome sequencing (WES) aiming to identify molecular markers useful to clinical practice. Libraries were prepared (Illumina Nextera exome Enrichment kit) for WES using the high quality DNA from tumor tissue and peripheral blood of each patient (HiSeq2500, Illumina). The coverage reached an average of 55x per sample. We used an in-house pipeline for cleaning, mapping and SNP calling revealing an average of 36,494 SNPs per sample. A paired comparison of normal and tumor samples was performed considering only the exclusive variants in tumors, after exclusion of the common variants, based on 1000 Genomes (http://www.1000genomes.org/), project and 6500 exomes (evs.gs.washington.edu/). It was identified 248 variants distributed in 169 genes, with 184 (74%) classified as new (variant not described) and 64 (26%) as rare (population frequency ≤0.1%). Three genes, ZNF717, HYDIN and KCNJ12, presented higher frequency of SNPs and were enriched to head and neck carcinoma (p = 1,9×10-9) and calcium (p = 1.82×10-3) pathways. Considering only tongue samples (4 cases) from non-smokers and HPV negative patients, the ZNF717 and HYDIN genes remained among those with the highest frequency of SNPs [non-smokers: HYDIN (23 SNPs) and ZNF77 (24 SNPs); HPV-negative: HYDIN (6 SNPs) and ZNF77 (5 SNPs)]. These genes are putative drivers in young patients with HNSCC.

Financial Support: FAPESP (2013/06897-2) and INCiTO (FAPESP: 2008/57887-9 and CNPq 573589/08-9)

Citation Format: Priscila Mayrink Miranda, Fabio A. Marchi, Maísa Pinheiro, Luiz Paulo Kowalski, Silvia Regina Rogatto. Tracking genomic alterations in young patients with head and neck carcinomas using whole-exome sequencing. [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 4915. doi:10.1158/1538-7445.AM2015-4915

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.

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 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.

Abstract 5134: Integrative analysis of gene expression, CpG island methylation, miRNA and gene copy number in cancer

Recently, a large number of specific genomic alterations between individuals have been described in cancer studies. Despite of these advances, the impact of several aberrations in the patient's physiology is still poorly defined. We have developed a method that integrates genomic, transcriptomic and epigenetic alterations by detecting key mutations that drive cancer progression. Our score guided algorithm searches for genes that are both recurrently aberrant in copy number, miRNA and methylation data and associated with variance of expression patterns in tumor samples. This proposed method uses concepts derived from gene network inference and address a recurrent problem in this approach. Usually, the main limitation of network inference methods is related a small number of samples with large dimensionalities and the noisy nature of the expression measurements. To address these limitations, alternatives are necessary to obtain better accuracy on the inference problem. One of them, presented in this study, is the integration of different data in order to reduce errors during the gene prediction. The algorithm has a regulatory module separated into layers that contains four-dimensional dataset consisting of gene expression, CGH-array, large-scale methylation and miRNA expression profiles measured on the same samples. Weights are applied in the data matrices, selecting the genes of different layers that are likely to contribute jointly to a specific gene expression profile. To identify key gene predictors the algorithm selects the best combination with the highest score, and also considers the role of rare copy number variation, amplification and homozygous deletion. In the context of the gene interaction network, the algorithm performs a protein-protein interaction (PPI) with the selected genes and the “hubs” are also connected to their associated aberrant neighbors, allowing the study of gene alteration pathway. With the aim to test this score-based algorithm, it was used 31 penile carcinomas model. Penile cancer is a rare neoplasm usually associated with low socioeconomic status, poor personal hygiene and HPV infection (particularly 16 and 18 subtypes in 40-50% of cases). Our analysis identified some regions with known and recurring alterations related to immune response and inflammation pathway, such as JUN (transcript downexpression, hypermethylation, and miR-133/miR-204/miR-139 overexpression) and IL-22 (copy number gains, transcript overexpression, miR-155 overexpression). miR-155 overexpression is reported as responsible for enhanced tumor growth and IL-22 overexpression. DNMT1 presented the best score in HPV positive cases, with transcript overexpression, hypomethylation and hsa-let-7c overexpression. In overall, these data demonstrate the ability of the integrative data algorithm to identify drivers in penile carcinogenesis.

Citation Format: Fabio A. Marchi. Integrative analysis of gene expression, CpG island methylation, miRNA and gene copy number in cancer. [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 5134. doi:10.1158/1538-7445.AM2013-5134

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 3984: An integrated approach to study large-scale expression analysis, copy number alterations and epigenetic profiles in cancer

Recently, some studies have integrated the results of copy number alterations and analysis of transcripts aiming to identify mutations in genes that may be drivers on the tumor process. Similarly, several studies in cancer have been described using an integrated analysis between transcripts expression and methylation data. In this study it was developed a method that integrates genomic and transcriptomic alterations by detecting key mutations that drive cancer progression. The score-guided algorithm search for genes that are both recurrently aberrant in copy number and methylation data and associated with variance of expression patterns in tumor samples. This proposed method uses concepts derived from gene network inference and addresses a recurring problem in this approach. Usually, the main limitation of network inference methods is related to a small number of samples with large dimensionalities and the noisy nature of the expression measurements. To address these limitations, alternatives are necessary to obtain better accuracy on the inference problem. One of them, presented in this study, is the integration of different data in order to reduce errors during the gene prediction by feature selection methods based on conditional entropy for identification of gene network architectures. To search the key genes predictors, the score-guided algorithm is based in three databases aiming to select the best combination with the highest score, weighted by the gene expression matrix. This method may allow greater accuracy decreasing the error during the network prediction and selecting only relevant “hub” genes in the analysis. To test this score-based algorithm, it was used a 35 penile carcinomas as study model evaluated by large-scale transcript analysis, CGH-array and large-scale methylation data. Penile cancer is a rare neoplasm usually associated with low socioeconomic status, poor personal hygiene and HPV infection (particularly 16 and 18 subtypes in 40-50% of cases). The analysis correctly identifies known recurrent regions with copy number and methylation changes related to immune response and inflammation pathways. In addition, the “hub” genes in these regions were also connected to their associated aberrant neighbors. Since the penile carcinoma development is often attributed to inflammatory and irritative effects of smegma - a bioproduct of bacterial action in penile epithelial cells described as associated with this tumor - the present findings may contribute to a better understanding of the tumor development process by identification of key factors in the regulation of gene expression and genome stability. Thus the findings presented in this study demonstrate the ability of the integrative data algorithm to identify drivers as biomarkers in penile carcinomas.

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 3984. doi:1538-7445.AM2012-3984

Abstract 3050: Detection of recurrent genomic alterations using array-CGH and high resolution-CGH in esophageal squamous cell carcinoma (ESCC)

Esophageal squamous cell carcinoma (ESCC) is the 8th most common cancer worldwide and the 6th tumor in frequency in Brazil. Most of cases are diagnosed at an advanced stage and despite the improvement of various treatment modalities the overall survival rates still remain low. The aim of this study was to identify the recurrent genomic alterations in ESCC using comparative genomic hybridization (CGH) and to correlate these findings with clinicopathological data. High resolution-comparative genomic hybridization (HR-CGH) was performed in 21 FFPE tissue samples. Array-CGH (aCGH) was carried out in 18 frozen tissue samples using the Agilent Human Genome CGH Microarray 44K following the manufacturer's protocol. Data were extracted and flagged with Feature Extraction (version 10.1.1.1), processed using Genomic Workbench Standard (version.5.0.14), with the statistical algorithm ADM-2 and sensitivity threshold of 5.0. At least three consecutive probes should be present to consider a region as containing copy number variation. Matched samples (FFPE and frozen tissue samples) from nine cases were evaluated by both methodologies. The HR-CGH analysis revealed 155 alterations in minimal common regions including 111 losses and 44 genomic gains. Gains at 1q12-q13 and losses at 3p24, 3p25 and 13q31 were significantly associated with lymph node metastasis. Gains at 1q22-q23 and 6q21 and losses at 19q13.1-13.2 were frequently detected in more differentiated (G1/G2) tumor samples. Losses at 3p25 and 15q25-26 showed significant association with earlier TNM stages. Loss at 12q24.3 was associated with cases without lymphatic invasion. The aCGH analysis revealed 38 significant genomic alterations including 21 gains and 17 losses. Gains were detected at 3q, 8q and 11q; losses were found at 3q, 5q, 8q, 9p, 14q, 19p and 21q. The genomic alterations included about 730 genes related to various cellular processes as cell cycle control, cell growth and adhesion, gene transcription and others. Genomic gains at 11q13.2-q13.3 were the most frequent alterations between the cases and gains at 11q13.2 showed significant association (p=0,022) with lymphatic invasion. Genes involved in cell cycle control (CCND1), growth factor (FGF3, -4, -19), Wnt signaling pathway (LRP5) and cell motility (CTTN) are mapped to these regions. Gains at 11q13.2, 11q13.2-q13.3, 11q13.3, and losses at 5q35.2, 9p23-p21.3, 9p21.3, 9p21.3-p21.1, 9p13.3-p13.1, 14q32.12 and 19q13.11 were identified by both aCGH and HR-CGH techniques, suggesting a relevance to these alterations in ESCC development. In this study, it was detected recurrent chromosomal alterations including genes involved in regulation of transcription, signal transduction, cell cycle, cell proliferation and differentiation that could have an impact on tumor development or progression in ESCC.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3050. doi:10.1158/1538-7445.AM2011-3050

Abstract 2144: An integrated genomic and transcriptomic analysis of human uterine leiomyomas

Uterine leiomyoma (UL) are tumors that arise from the uterine smooth muscle wall. Despite their nonmalignant nature, UL represent a major concern in women's health through their induction of significant morbidity in more than 25% of reproductive-age. The etiology of UL remains unknown. Cytogenetic studies have been identified recurrent aberrations involving the t(12;14); del(7)(q22q32); trisomy 12; and 6p21 rearrangements. The aim of this study was integrate genomic and gene expression microarray data to identify genes with altered function due to genomic instability. DNA and RNA were extracted from 24 UL from women at proliferative (n=14) and secretory (n=10) phase of the menstrual cycle. Normal control RNA was obtained from adjacent myometrium from all cases. Array CGH and gene expression microarray was done using the Human 44K Agilent oligoarrays according to manufacturer's instructions. Data were extracted and flagged with Feature Extraction software (version 10.1.1.1) and processed using Genomic Workbench Standard (version.5.0.14). Non-supervised analysis of gene expression revealed clustering of all cases independent of the phase of menstrual cycle. It was observed a significant correlation between deletion and down expression at 1q32.2-q44 and 7q11.22-q33. Although deletions at 1q and 7q had been described previously as involved in UL, the genes mapped at these regions were poorly studied. These genes are involved in Wnt signaling pathway, induction of apoptosis, transforming growth factor signaling pathway, fumarate hydratase activity, and fibrinolysis. Furthermore, it was observed correlation between amplification and increased gene expression at 11p15.5, 14q32.33, and 16p13.3. These regions harboring genes with function associated with regulation of cell proliferation and regulation of JNK cascade. Our results provide strong circumstantial evidence that different patterns of genomic imbalances contribute to their specific transcriptomic profiles. In the future, new therapies based on these findings can be applied in a subgroup of patients with specific genomic imbalances.

Supported by the FAPESP (07/51643-8) and CNPq (485032/2007-4), Brazil.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2144.