Genomic Profiling of Advanced-Stage Oral Cancers Reveals Chromosome 11q Alterations as Markers of Poor Clinical Outcome

Identifying oral cancer lesions associated with high risk of relapse and predicting clinical outcome remain challenging questions in clinical practice. Genomic alterations may add prognostic information and indicate biological aggressiveness thereby emphasizing the need for genome-wide profiling of oral cancers. High-resolution array comparative genomic hybridization was performed to delineate the genomic alterations in clinically annotated primary gingivo-buccal complex and tongue cancers (n = 60). The specific genomic alterations so identified were evaluated for their potential clinical relevance. Copy-number changes were observed on chromosomal arms with most frequent gains on 3q (60%), 5p (50%), 7p (50%), 8q (73%), 11q13 (47%), 14q11.2 (47%), and 19p13.3 (58%) and losses on 3p14.2 (55%) and 8p (83%). Univariate statistical analysis with correction for multiple testing revealed chromosomal gain of region 11q22.1–q22.2 and losses of 17p13.3 and 11q23–q25 to be associated with loco-regional recurrence (P = 0.004, P = 0.003, and P = 0.0003) and shorter survival (P = 0.009, P = 0.003, and P 0.0001) respectively. The gain of 11q22 and loss of 11q23-q25 were validated by interphase fluorescent in situ hybridization (I-FISH). This study identifies a tractable number of genomic alterations with few underlying genes that may potentially be utilized as biological markers for prognosis and treatment decisions in oral cancers

Combining chromosomal arm status and significantly aberrant genomic locations reveals new cancer subtypes

Many types of tumors exhibit chromosomal losses or gains, as well as local amplifications and deletions. Within any given tumor type, sample specific amplifications and deletionsare also observed. Typically, a region that is aberrant in more tumors,or whose copy number change is stronger, would be considered as a more promising candidate to be biologically relevant to cancer. We sought for an intuitive method to define such aberrations and prioritize them. We define V, the volume associated with an aberration, as the product of three factors: a. fraction of patients with the aberration, b. the aberrations length and c. its amplitude. Our algorithm compares the values of V derived from real data to a null distribution obtained by permutations, and yields the statistical significance, p value, of the measured value of V. We detected genetic locations that were significantly aberrant and combined them with chromosomal arm status to create a succint fingerprint of the tumor genome. This genomic fingerprint is used to visualize the tumors, highlighting events that are co ocurring or mutually exclusive. We allpy the method on three different public array CGH datasets of Medulloblastoma and Neuroblastoma, and demonstrate its ability to detect chromosomal regions that were known to be altered in the tested cancer types, as well as to suggest new genomic locations to be tested. We identified a potential new subtype of Medulloblastoma, which is analogous to Neuroblastoma type 1.Comment: 34 pages, 3 figures; to appear in Cancer Informatic

Microarrays in molecular profiling of cancer : focus on head and neck squamous cell carcinoma

Microarrays have a wide range of applications in the biomedical field. From the beginning, arrays have mostly been utilized in cancer research, including classification of tumors into different subgroups and identification of clinical associations. In the microarray format, a collection of small features, such as different oligonucleotides, is attached to a solid support. The advantage of microarray technology is the ability to simultaneously measure changes in the levels of multiple biomolecules. Because many diseases, including cancer, are complex, involving an interplay between various genes and environmental factors, the detection of only a single marker molecule is usually insufficient for determining disease status. Thus, a technique that simultaneously collects information on multiple molecules allows better insights into a complex disease. Since microarrays can be custom-manufactured or obtained from a number of commercial providers, understanding data quality and comparability between different platforms is important to enable the use of the technology to areas beyond basic research. When standardized, integrated array data could ultimately help to offer a complete profile of the disease, illuminating mechanisms and genes behind disorders as well as facilitating disease diagnostics. In the first part of this work, we aimed to elucidate the comparability of gene expression measurements from different oligonucleotide and cDNA microarray platforms. We compared three different gene expression microarrays; one was a commercial oligonucleotide microarray and the others commercial and custom-made cDNA microarrays. The filtered gene expression data from the commercial platforms correlated better across experiments (r=0.78-0.86) than the expression data between the custom-made and either of the two commercial platforms (r=0.62-0.76). Although the results from different platforms correlated reasonably well, combining and comparing the measurements were not straightforward. The clone errors on the custom-made array and annotation and technical differences between the platforms introduced variability in the data. In conclusion, the different gene expression microarray platforms provided results sufficiently concordant for the research setting, but the variability represents a challenge for developing diagnostic applications for the microarrays. In the second part of the work, we performed an integrated high-resolution microarray analysis of gene copy number and expression in 38 laryngeal and oral tongue squamous cell carcinoma cell lines and primary tumors. Our aim was to pinpoint genes for which expression was impacted by changes in copy number. The data revealed that especially amplifications had a clear impact on gene expression. Across the genome, 14-32% of genes in the highly amplified regions (copy number ratio >2.5) had associated overexpression. The impact of decreased copy number on gene underexpression was less clear. Using statistical analysis across the samples, we systematically identified hundreds of genes for which an increased copy number was associated with increased expression. For example, our data implied that FADD and PPFIA1 were frequently overexpressed at the 11q13 amplicon in HNSCC. The 11q13 amplicon, including known oncogenes such as CCND1 and CTTN, is well-characterized in different type of cancers, but the roles of FADD and PPFIA1 remain obscure. Taken together, the integrated microarray analysis revealed a number of known as well as novel target genes in altered regions in HNSCC. The identified genes provide a basis for functional validation and may eventually lead to the identification of novel candidates for targeted therapy in HNSCC.Biolääketieteessä mikrosiruilla tutkitaan samanaikaisesti tuhansia molekyylejä solu- tai kudosnäytteestä. Mikrosirut koostuvat kiinteällä alustalla, kuten mikroskooppilasilla, olevista tuhansista pienistä pisteistä. Jokainen piste voi sisältää esimerkiksi 25-60 emäksen pituisia oligonukleotidejä, jotka vastaavat tiettyä geeniä. Näin mikrosirujen avulla voidaan tutkia vaikkapa useiden geenien ilmentymistä näytteestä. Mikrosiruilla on paljon sovelluksia biolääketieteen alalla. Erityisesti siruja on käytetty syöpätutkimuksessa. Mikrosiruja geenien ilmentymisen määrittämiseen valmistetaan paikallisesti tutkimuslaboratoriossa tai ostetaan kaupallisilta valmistajilta. Kaupallisia valmistajia on useita. Monimuotoisuus asettaa haasteita tiedon keräämiselle eri sirutyypeiltä ja kerätyn tiedon vertaamiselle. Tässä väitöskirjatyössä verrattiin geenien ilmentymisen tuloksia kolmelta erityyppiseltä mikrosirulta. Joukossa oli kaksi kaupallista sekä yksi itsetehty siru. Vertailu osoitti, että kaupalliset sirut antoivat samankaltaisempia tuloksia, korrelaatio sirujen välillä 0.78-0.86, kuin itsetehty siru. Vaikka tulokset osoittivat, että eri siruilta voidaan saada vertailukelpoista tietoa, ei vertailu tulosten välillä ole suoraviivaista. Haasteena ovat mikrosirujen tekniset eroavaisuudet sekä tiedon saattaminen vertailukelpoiseen muotoon. Mikrosirujen kehittyessä tutkimustyökalusta kliinisiin sovelluksiin standardoinnilla - ja sitä kautta tulosten paremmalla vertautuvuudella - on tärkeä tehtävä. Työssä tutkittiin myös biologisen tiedon yhdistämistä eri mikrosirumenetelmistä pään ja kaulan alueen syövässä. Mittaamalla mikrosiruilla geenin kopiomäärän muutoksia DNA-tasolla ja yhdistämällä tämä tieto geenin ilmentymistason muutoksiin saatiin tietoa syövälle merkityksellisistä geeneistä. Erityisesti korkeasteiset kopioluvun muutokset vaikuttivat geenien ilmentymiseen, sillä 14-32% näillä alueilla sijaisevista geeneistä oli myös kohonnut ilmentymistaso. Tilastollisin menetelmin osoitettiin satoja geenejä, joilla kopioluvun ja ilmentymän muutos näyttävät olevan yhteydessä toisiinsa. Tässä joukossa oli uusia kohdegeenejä ennestään tunnetuille kromosomialueille, kuten FADD ja PPFIA1 geenit kromosomissa 11. Työssä tunnistetut geenit antavat hyvän pohjan jatkotutkimuksille, jotka voivat vuosien kuluessa johtaa edistysaskeliin pään ja kaulan alueen syövän hoidossa

A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array

<p>Abstract</p> <p>Background</p> <p>DNA copy number aberration (CNA) is one of the key characteristics of cancer cells. Recent studies demonstrated the feasibility of utilizing high density single nucleotide polymorphism (SNP) genotyping arrays to detect CNA. Compared with the two-color array-based comparative genomic hybridization (array-CGH), the SNP arrays offer much higher probe density and lower signal-to-noise ratio at the single SNP level. To accurately identify small segments of CNA from SNP array data, segmentation methods that are sensitive to CNA while resistant to noise are required.</p> <p>Results</p> <p>We have developed a highly sensitive algorithm for the edge detection of copy number data which is especially suitable for the SNP array-based copy number data. The method consists of an over-sensitive edge-detection step and a test-based forward-backward edge selection step.</p> <p>Conclusion</p> <p>Using simulations constructed from real experimental data, the method shows high sensitivity and specificity in detecting small copy number changes in focused regions. The method is implemented in an R package FASeg, which includes data processing and visualization utilities, as well as libraries for processing Affymetrix SNP array data.</p

Genomic imbalances in esophageal squamous cell carcinoma identified by molecular cytogenetic techniques

This review summarizes the chromosomal changes detected by molecular cytogenetic approaches in esophageal squamous cell carcinoma (ESCC), the ninth most common malignancy in the world. Whole genome analyses of ESCC cell lines and tumors indicated that the most frequent genomic gains occurred at 1, 2q, 3q, 5p, 6p, 7, 8q, 9q, 11q, 12p, 14q, 15q, 16, 17, 18p, 19q, 20q, 22q and X, with focal amplifications at 1q32, 2p16-22, 3q25-28, 5p13-15.3, 7p12-22, 7q21-22, 8q23-24.2, 9q34, 10q21, 11p11.2, 11q13, 13q32, 14q13-14, 14q21, 14q31-32, 15q22-26, 17p11.2, 18p11.2-11.3 and 20p11.2. Recurrent losses involved 3p, 4, 5q, 6q, 7q, 8p, 9, 10p, 12p, 13, 14p, 15p, 18, 19p, 20, 22, Xp and Y. Gains at 5p and 7q, and deletions at 4p, 9p, and 11q were significant prognostic factors for patients with ESCC. Gains at 6p and 20p, and losses at 10p and 10q were the most significant imbalances, both in primary carcinoma and in metastases, which suggested that these regions may harbor oncogenes and tumor suppressor genes. Gains at 12p and losses at 3p may be associated with poor relapse-free survival. The clinical applicability of these changes as markers for the diagnosis and prognosis of ESCC, or as molecular targets for personalized therapy should be evaluated

Caracterização genética e epigenética do carcinoma da laringe

Mestrado em Biomedicina MolecularLaryngeal carcinomas belong to a bigger family of tumours known as Head and Neck Cancer (HNC). HNC is the sixth most malignant type of cancer in the world and it can arise from several anatomical sites. Among them, the larynx is the second most common affect organ. The incidence of laryngeal carcinoma is 1,9% worldwide and it presents a high mortality rate (1,6%). Despite technological advances in diagnosis and treatment fields, the 5 year-survival rate did not improved significantly. The low survival rates are mainly explained by a late diagnosis, tumour aggressiveness and the fact that laryngeal carcinoma metastasize easily. Taking this into consideration, it is essential to identify biomarkers with significant diagnostic and prognostic value in order to anticipate the detection of laryngeal carcinoma in an early stage. This study arises mainly for characterize the genetic and epigenetic profile of laryngeal squamous cell carcinoma (LSCC). Eight LSCC samples and seven non-tumour samples contralateral to the primary tumour were collected upon resection surgery and characterized by MLPA, MS-MLPA and array CGH. The results showed that gain of genetic material was mainly present in chromosomes 3q, 8q, 11q, 14q13.1, Xp22.31 and Xq21.1 while genetic loss occurred mainly in chromosomes 3p, 9p23.1 and Y. Gain of MYC and TNFRSF1A was the most common event among the tumour samples included in this study. Regarding the methylation profile, the genes CDKN2A, CHFR, RARβ e RASSF1 were the only ones which were methylated in this samples. In conclusion, this study allowed to identify genetic alterations associated with LSCC that have already been reported in scientific papers as well as alterations that have been associated with tumour development and progression. In addition, a few genetic alterations which have never been reported as being associated with human cancer before were identified. Nevertheless, new studies must be carried out, with a higher number of samples. Ultimately, the main goal would be to identify genetic alterations significantly associated with LSCC progression and establish a correlation with clinicopathological data.O carcinoma da laringe pertence a uma grande família de tumores conhecida como Cancro da Cabeça e do Pescoço que é considerado o sexto tipo de tumor mais maligno em todo o mundo. Dentro desta família, os tumores podem ter origem em diversos locais anatómicos, sendo a laringe o segundo órgão mais comummente afetado. O cancro da laringe apresenta uma incidência mundial de 1,9% e uma taxa de mortalidade elevada de 1,6%. Apesar dos avanços tecnológicos na área do diagnóstico e da terapêutica, a taxa de sobrevivência ao fim de 5 anos não apresentou melhorias significativas. As baixas taxas de sobrevivências são explicadas essencialmente pelo diagnóstico tardio, pela agressividade do tumor e pela sua propensão a desenvolver metástases. Desta forma, torna-se essencial a identificação de biomarcadores com valor de diagnóstico e prognóstico a fim de detetar a presença do tumor numa fase mais precoce. Este estudo surge com o objetivo principal de caracterizar o perfil genético e epigenéticos do carcinoma das células escamosas da laringe com recurso às técnicas de MLPA, MS-MLPA e array CGH, usando oito amostras tumorais e sete amostras não-tumorais contra laterais ao tumor, ambas coletadas após cirurgia A análise genética revelou uma maior taxa de ganho de material genético nos cromossomas 3q, 8q, 11q, 14q13.1, Xp22.31, Xq21.1 e perda de material genético nos cromossomas 3p, 9p23.1 e Y. O ganho dos genes MYC e TNFRSF1A revelou ser o evento mais comum entre as amostras analisadas. Relativamente ao perfil epigenético, observou-se que os genes CDKN2A, CHFR, RARβ e RASSF1 se encontravam metilados nas amostras em estudo. Em suma, este trabalho permitiu identificar algumas alterações genéticas e epigenéticas descritas na literatura como estando associadas ao CCEL, assim como alterações associadas ao desenvolvimento tumoral. Foram ainda identificadas alterações que ainda não foram reportadas como estando associadas ao cancro. Desta forma, este estudo piloto permitiu dar início ao estudo de potenciais biomarcadores associados ao CCEL. Porém, novos estudos devem ser realizados, com um número de amostras superior, de forma a identificar alterações genéticas significativas no desenvolvimento e progressão do CCEL e associa-las às características clinico patológicas dos doentes

Tumor Transcriptome Sequencing Reveals Allelic Expression Imbalances Associated with Copy Number Alterations

Due to growing throughput and shrinking cost, massively parallel sequencing is rapidly becoming an attractive alternative to microarrays for the genome-wide study of gene expression and copy number alterations in primary tumors. The sequencing of transcripts (RNA-Seq) should offer several advantages over microarray-based methods, including the ability to detect somatic mutations and accurately measure allele-specific expression. To investigate these advantages we have applied a novel, strand-specific RNA-Seq method to tumors and matched normal tissue from three patients with oral squamous cell carcinomas. Additionally, to better understand the genomic determinants of the gene expression changes observed, we have sequenced the tumor and normal genomes of one of these patients. We demonstrate here that our RNA-Seq method accurately measures allelic imbalance and that measurement on the genome-wide scale yields novel insights into cancer etiology. As expected, the set of genes differentially expressed in the tumors is enriched for cell adhesion and differentiation functions, but, unexpectedly, the set of allelically imbalanced genes is also enriched for these same cancer-related functions. By comparing the transcriptomic perturbations observed in one patient to his underlying normal and tumor genomes, we find that allelic imbalance in the tumor is associated with copy number mutations and that copy number mutations are, in turn, strongly associated with changes in transcript abundance. These results support a model in which allele-specific deletions and duplications drive allele-specific changes in gene expression in the developing tumor

Genetic and functional analysis of head and neck carcinogenesis

Brakenhoff, R.H. [Promotor]Leemans, C.R. [Promotor]Braakhuis, B.J.M. [Copromotor]Ylstra, B. [Copromotor

Dos genes à radiorresistência no cancro da cabeça e pescoço

Mestrado em Biomedicina MolecularHead and Neck Cancers (HNC) are a group of tumours located in the upper aero-digestive tract. Head and Neck Squamous Cell Carcinoma (HNSCC) represent about 90% of all HNC cases. It has been considered the sixth most malignant tumour worldwide and, despite clinical and technological advances, the five-year survival rate has not improved much in the last years. Nowadays, HNSCC is well established as a heterogeneous disease and that its development is due to accumulation of genetic events. Apart from the majority of the patients being diagnosed in an advanced stage, HNSCC is also a disease with poor therapeutic outcome. One of the therapeutic approaches is radiotherapy. However, this approach has different drawbacks like the radioresistance acquired by some tumour cells, leading to a worse prognosis. A major knowledge in radiation biology is imperative to improve this type of treatment and avoid late toxicities, maintaining patient quality of life in the subsequent years after treatment. Then, identification of genetic markers associated to radiotherapy response in patients and possible alterations in cells after radiotherapy are essential steps towards an improved diagnosis, higher survival rate and a better life quality. Not much is known about the radiation effects on cells, so, the principal aim of this study was to contribute to a more extensive knowledge about radiation treatment in HNSCC. For this, two commercial cell lines, HSC-3 and BICR-10, were used and characterized resorting to karyotyping, aCGH and MS-MLPA. These cell lines were submitted to different doses of irradiation and the resulting genetic and methylation alterations were evaluated. Our results showed a great difference in radiation response between the two cell lines, allowing the conclusion that HSC-3 was much more radiosensitive than BICR-10. Bearing this in mind, analysis of cell death, cell cycle and DNA damages was performed to try to elucidate the motifs behind this difference. The characterization of both cell lines allowed the confirmation that HSC-3 was derived from a metastatic tumour and the hypothesis that BICR-10 was derived from a dysplasia. Furthermore, this pilot study enabled the suggestion of some genetic and epigenetic alterations that cells suffer after radiation treatment. Additionally, it also allowed the association of some genetic characteristics that could be related to the differences in radiation response observable in this two cell lines. Taken together all of our results contribute to a better understanding of radiation effects on HNSCC allowing one further step towards the prediction of patients’ outcome, better choice of treatment approaches and ultimately a better quality of life.Cancro da Cabeça e Pescoço refere-se a um grupo de tumores que aparecem no trato aerodigestivo superior, sendo que o carcinoma das células escamosas da cabeça e pescoço (CCECP) corresponde a mais de 90% de todos os casos de cancro nesta região. Foi considerado o sexto tumor mais maligno em todo o mundo e, apesar de todos os avanços tecnológicos e clínicos, a taxa de sobrevivência a cinco anos não melhorou significativamente nas últimas décadas. Atualmente sabe-se que o CCECP é uma doença bastante heterogénea que se desenvolve devido à acumulação de alterações genéticas e epigenéticas. Alguns dos grandes problemas associados a este tipo de cancro são o diagnóstico em fase tardia da doença e os poucos resultados terapêuticos. Uma das escolhas terapêuticas para o CCECP é a radioterapia, no entanto, esta tem diversos inconvenientes, como a radioresistência adquirida por algumas células tumorais, que se associam a piores prognósticos. Um aumento do conhecimento na área da biologia da radiação é necessário para melhorar esta opção terapêutica, evitando futuros efeitos tóxicos e fornecendo uma melhor qualidade de vida nos anos subsequentes ao tratamento. Desta forma, a identificação de marcadores moleculares associados quer a uma resposta à radioterapia, quer a possíveis alterações celulares após tratamento com radiação, é essencial para melhorar o diagnóstico, taxa de sobrevivência e qualidade de vida destes doentes. Adicionalmente, existe uma grande falha no conhecimento em relação aos efeitos da radiação nas células, como tal, o principal objetivo deste estudo foi o de contribuir para um conhecimento mais alargado do efeito da radiação em doentes com CCECP. Para isso foram utilizadas duas linhas comerciais celulares, HSC-3 (derivada de um tumor metastático da língua) e BICR-10 (derivada de um tumor da mucosa bucal), que foram caracterizadas com recurso a aCGH, MS-MLPA e citogenética convencional. Estas linhas foram submetidas a diferentes doses de radiação e as alterações genéticas e de metilação pós tratamento foram determinadas. Estes resultados demonstraram uma grande variação de resposta à radiação para estas duas linhas celulares, permitindo a conclusão que a linha HSC-3 é mais radiossensível que a linha BICR-10. Tendo isto em mente, procedeu-se a análise da morte celular, ciclo celular e danos no DNA de forma a tentar compreender esta diferença. A caracterização genética de ambas as linhas celulares permitiu corroborar que a linha HSC-3 era derivada de um tumor metastático e sugeriu que a linha celular BICR-10 estaria associada a um estado de displasia. Para além disto, foi possível analisar alterações genéticas e epigenéticas ocorridas após irradiação e associar determinados perfis genéticos a uma melhor ou pior resposta à radiação. Em suma, os nossos resultados contribuiram para um conhecimento mais aprofundado dos efeitos da radiação no CCECP possibilitando, no futuro, melhores opções de tratamento e uma melhor qualidade de vida para estes doentes