Enriquecimiento de mutaciones en el cáncer de mama triple negativo metastásico

Antecedentes: El Cáncer de Mama Triple Negativo (TNBC) es una enfermedad heterogénea con biología agresiva y evolución tumoral compleja. El propósito fue identificar el enriquecimiento de las alteraciones genómicas del Cáncer de Mama Triple Negativo Metastásico (mTNBC). Métodos: Se recuperaron datos genómicos de 550 tumores TNBC primarios del “Consorcio Internacional de Taxonomía Molecular del Cáncer de Mama” (METABRIC) y los conjuntos de datos Atlas de Genoma del Cáncer (TCGA), 58 tumores mTNBC del "Perfil Mutacional de Cánceres de mama metastásicos" y "El Proyecto de cáncer de mama metastásico". El análisis estadístico de los datos de Microarrays entre tumores primarios y metastásicos se realizó mediante una prueba del Chicuadrado, y se estimó el porcentaje de enriquecimiento de mutaciones en mTNBC. Los valores de P se ajustaron para pruebas múltiples con el método Benjamini-Hochberg con una tasa de falso descubrimiento (FDR) <0.5. Además, identificamos las características del cáncer en mTNBC. Resultados: Siete genes TTN, HMCN1, RELN, PKHD1L1, DMD, FRAS1 y RYR3 se enriquecieron en mTNBC después de aplicar la prueba múltiple. Solo la amplificación RPS6KB2 fue estadísticamente significativa; por el contrario, los genes TET1, RHOA, EPHA5, SET, KCNJ5, ABCG4, NKX3-1, SDHB, IGF2 y BRCA1 fueron los más frecuentes. La alteración molecular relacionada a las características del cáncer fue la "inestabilidad genética y mutación". Sin embargo, la "activación de la destrucción inmune" fue el menos representado. Conclusión: A pesar de las limitaciones del estudio, se identificaron patrones recurrentes de alteraciones genómicas con posible contribución en la evolución del tumo

Exploring the relationship between abnormally high expression of NUP205 and the clinicopathological characteristics, immune microenvironment, and prognostic value of lower-grade glioma

Nuclear pore complex (NPC) is a major transport pivot for nucleocytoplasmic molecule exchange. Nucleoporin 205 (NUP205)—a main component of NPC—plays a key regulatory role in tumor cell proliferation; however, few reports document its effect on the pathological progression of lower-grade glioma (LGG). Therefore, we conducted an integrated analysis using 906 samples from multiple public databases to explore the effects of NUP205 on the prognosis, clinicopathological characteristics, regulatory mechanism, and tumor immune microenvironment (TIME) formation in LGG. First, multiple methods consistently showed that the mRNA and protein expression levels of NUP205 were higher in LGG tumor tissue than in normal brain tissue. This increased expression was mainly noted in the higher WHO Grade, IDH-wild type, and 1p19q non-codeleted type. Second, various survival analysis methods showed that the highly expressed NUP205 was an independent risk indicator that led to reduced survival time of patients with LGG. Third, GSEA analysis showed that NUP205 regulated the pathological progress of LGG via the cell cycle, notch signaling pathway, and aminoacyl-tRNA biosynthesis. Ultimately, immune correlation analysis suggested that high NUP205 expression was positively correlated with the infiltration of multiple immune cells, particularly M2 macrophages, and was positively correlated with eight immune checkpoints, particularly PD-L1. Collectively, this study documented the pathogenicity of NUP205 in LGG for the first time, expanding our understanding of its molecular function. Furthermore, this study highlighted the potential value of NUP205 as a target of anti-LGG immunotherapy

Exploration of the Immune Landscape of EBV-associated Gastric Cancers

Epstein–Barr virus (EBV) is a gammaherpesvirus associated with 9% of all gastric cancers (GCs). EBV-associated GCs (EBVaGCs) are pathologically and clinically distinct entities from EBV-negative GCs (EBVnGCs), with EBVaGCs exhibiting differential molecular pathology and patient prognosis. The purpose of this thesis is to investigate the tumor microenvironment (TME) of EBVaGCs, which has not been explored in-depth. We hypothesize that EBVaGCs and EBVnGCs are also distinct in terms of the molecular immune landscape. We employed over 400 stomach adenocarcinoma (STAD) samples from The Cancer Genome Atlas (TCGA), as well as a single cell dataset, for the construction of a web suite of tools exploring multimodal data for GCs, and the exploration of changes in the TME of EBVaGCs and cellular phenotypes overrepresented in EBVaGCs. Our findings confirm the distinctness of EBVaGCs and EBVnGCs, with EBV-positive status possibly being a potential biomarker for the application of immunotherapy in GC

A Situação do Câncer de Pele em Missal, PR: Investigação de Mutações no Gene CDKN2A Relacionado ao Melanoma na População

Dissertação de mestrado apresentada ao Programa de Pós-Graduaçãoem Biociências, do Instituto Latino-Americano de Ciências da Vida e da Natureza, da Universidade Federal da Integração Latino-Americana, como requisito parcial à obtenção do título de Mestre em Ciências, área de concentração Biociências.Durante as últimas décadas, o município de Missal, localizado no oeste paranaense, apresentou um grande aumento na incidência de câncer na população e dados de 2016 demonstraram que o câncer é a segunda maior causa de óbito da região. O câncer de pele é um dos mais prevalentes no município e representa 30% de todos os tumores malignos do Brasil. Portanto, o objetivo desta pesquisa foi compreender os fatores relacionados aos cânceres de pele em Missal, especialmente o melanoma, e investigar alterações em genes CDKN2A, CDK4 e MITF relacionados ao melanoma hereditário em moradores do município. A prevalência do melanoma é de 0.08%, sendo 0.03% do sexo masculino e 0.05% do sexo feminino. A ocorrência é de 84/100mil habitantes, sendo 27/100mil habitantes do sexo masculino e 57/100mil habitantes do sexo feminino. Ainda, 11% dos portadores de melanoma de Missal possui pelo menos um critério clínico para melanoma hereditário. Com relação ao câncer de pele não melanoma, a sua ocorrência é de 1.708/100mil habitantes, sendo 897/100mil habitantes do sexo masculino e 811/100mil habitantes do sexo feminino. Foi observado através do sequenciamento de DNA do gene CDKN2A apenas um SNP em um indivíduo portador de melanoma, sendo este uma substituição de uma guanina por uma adenina na posição 436 (c.436G>A) o qual afeta o éxon 3 do gene CDKN2A resultando em p.Asp146Asn. Sobre os resultados moleculares do MLPA foram verificados alterações nos genes CDKN2A, CDK4, MLLT3, MIR3 e MTAP. Ainda, as análises estatísticas relacionadas ao MLPA demonstraram que as variáveis analisadas contribuíram com menos de 10% cada uma para o surgimento do melanoma na população, o que evidencia o caráter multifatorial desta patologia e indica que os hábitos de vida estão intimamente ligados ao surgimento desta patologia nesta população, tais como a exposição contínua ou intermitente ao sol, a não utilização de fotoprotetores e os padrões alimentares.DS/UNILA (Demanda Social da Unila) CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) PBA (Programa Institucional de Pesquisa Básica e Aplicada) da Fundação Araucári

A transcriptomic and molecular approach uncovering ASCL2 as a novel tumourigenic gene in breast cancer

Breast cancer is highly heterogeneous and is considered a collection of molecularly distinct tumour subtypes. Substantial efforts have been made to explore the gene expression profiles underlying the subtypes, and to elucidate possible markers associated with clinical outcomes. However, research in this area has been met with significant challenges and despite ongoing advancements in diagnostics and targeted therapeutics, incidence and mortality continues to rise. Thus, there is a need for greater molecular characterisation of breast tumours, to further understand the mechanistic roles of genes within their respective signalling pathways. With the advent of high-throughput technologies in transcriptomics, as well as the use of open databases and bioinformatics analysis tools, it is now possible to examine thousands of genes in parallel, generating an unprecedented amount of information. This provides a means for researchers to identify novel genes and targets from large volumes of gene expression data. However, the task of extracting clinically relevant results, is a prominent challenge. Therefore, the aim of this study was to use a streamlined in silico pipeline, integrated with in vitro methods to identify and functionally investigate a novel genetic marker demonstrating a key role in breast carcinogenesis. Gene expression profiles from breast cancer cell lines were obtained from public databases (Array Express and Gene Expression Omnibus). Data was filtered and subjected to an extreme variation analysis to generate a list of differentially expressed genes. Subsequently, multiple pathway analysis tools were used to identify a novel candidate gene for further investigation. Achaete-scute complex homolog 2 (ASCL2) is a transcription factor and Wnt-target gene, recognised as a regulator of stem cell identity and embryogenesis. Gene expression was validated in vitro by Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR), and to assess the tumourigenic potential of ASCL2, siRNA knockdown was performed; assays were employed to measure proliferation, wound-healing and apoptosis. Data mining of patient tumours obtained from the METABRIC study was also undertaken to ascertain the potential of ASCL2 as a prognostic indicator. This work utilised a systematic pipeline used by the wider scientific community for the identification of candidate genes from transcriptomic data. Differential expression of ASCL2 was observed across multiple breast cancer cell lines, with largest the expression seen in MCF7 cells. Although evidence did not support the usage of ASCL2 as a prognostic indicator in patient tumours, data integrated from multiple lines of investigation suggested that this gene may influence the migratory capacity of breast tumour cells, whilst exercising its tumourigeneic function via the Wnt signalling pathway in breast cancer. Thus, this potential novel role of ASCL2 in breast tumourigenesis highlights a prominent area for further exploration

Pan-Cancer Analysis of Telomerase Reverse Transcriptase (TERT) Isoforms

Reactivation of the multi-subunit ribonucleoprotein telomerase is the primary telomere maintenance mechanism in cancer, but it is rate-limited by the enzymatic component, telomerase reverse transcriptase (TERT). While regulatory in nature, TERT alternative splice variant/isoform regulation and functions are not fully elucidated and are further complicated by their highly diverse expression. In this thesis, I characterized TERT expression across normal and neoplastic tissues using TCGA and GTEx RNA-sequencing data. In doing so, I demonstrated the global overexpression and splicing shift towards full-length TERT in neoplastic tissue. Furthermore, my studies identified tumour subtype expression differences possibly regulated by subtype-specific characteristics, detailed heterogeneity in both isoform function and prognostic potential and determined cancer cell lines with representative tumour specific TERT transcriptomes. Taken together, my work reinforced the need for tissue specific TERT investigations, provided avenues to do so, and brought to light the current technical limitations of bioinformatically analyzing TERT isoform expression