Loading...
5 results
Search Results
Now showing 1 - 5 of 5
- Discovery of novel mechanisms of centrosome amplification and their therapeutic value in cancerPublication . Almeida, Bernardo Lucas Carvalho Pereira de; Maia, Ana Teresa; Morais, Nuno BarbosaGenomic instability is a hallmark of cancer cells that generates the genetic diversity that makes possible the acquisition of all the other hallmarks. Thus, the maintenance of genome stability is critical for proper cell function. Centrosomes, the major microtubule-organising centres of animal cells, are the main subcellular organelles implicated in the maintenance of genome stability. It is therefore not surprising that centrosome amplification (CA) – the presence of more than one centrosome in a cell – is a common feature in cancer. Recent work from the Bettencourt-Dias Lab has identified a new recurrent feature of cancer cells: centriole over-elongation (COE), which also promotes CA. Those abnormalities are specific features of cancer cells and hence appealing targets in cancer therapy. However, their origins and therapeutic value remain poorly understood, preventing their use in the clinic. We have screened the NCI-60 panel of human cancer cell lines for centriole number and individual length to test their frequency and interdependence. We have thereby also generated a metric capturing each abnormality level per cell line that we then correlated with the publicly available molecular (particularly transcriptomic and proteomic) and drug-sensitivity quantitative profiles for that panel. Our work showed lower frequency of COE compared to CA and lung and skin as the primary cancer tissues with higher centriole length heterogeneity. However, the two features are not independent, with overly-longer centrioles being more common in cells with CA. Our single-cell analyses have also suggested that cells apparently do not control their overall centriolar mass when the centriole number increases. Moreover, cancer cell lines with longer centrioles proliferated slower due to an accumulation of cells in G1 phase, suggesting that centriole length defects could lead to a cell cycle delay in G1. In addition, our original genomewide approach highlighted putative mechanisms associated with both abnormalities in cancer, such as the PRKACA kinase promoting COE and the proteasome protecting cells from CA. Correlation with drug activity have both associated CA with higher sensitivity to compound activity and also identified some compounds as potential therapeutic options to selectively target cells with higher incidence of centriole abnormalities. This work provides the first single-centriole-level portrait of centriole abnormalities in cancer and contributes to the understanding of their molecular origins, namely by revealing novel molecular mechanisms in cell cycle biology. Given the cancer-specificity of these abnormalities, the identified compounds will inspire the development of clinical applications based on selectively targeting these Achilles’ heels of cancer cells.
- Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significantPublication . Correia, Lizelle; Magno, Ramiro; Xavier, JM; Almeida, Bernardo; Duarte, Isabel; Esteves, Filipa; Ghezzo, Marinella; Eldridge, Matthew; Sun, Chong; Bosma, Astrid; Mittempergher, Lorenza; Marreiros, Ana; Bernards, Rene; Caldas, Carlos; Chin, Suet-Feung; Maia, Ana-TeresaPIK3CA mutations are the most common in breast cancer, particularly in the estrogen receptor-positive cohort, but the benefit of PI3K inhibitors has had limited success compared with approaches targeting other less common mutations. We found a frequent allelic expression imbalance between the missense mutant and wild-type PIK3CA alleles in breast tumors from the METABRIC (70.2%) and the TCGA (60.1%) projects. When considering the mechanisms controlling allelic expression, 27.7% and 11.8% of tumors showed imbalance due to regulatory variants in cis, in the two studies respectively. Furthermore, preferential expression of the mutant allele due to cis-regulatory variation is associated with poor prognosis in the METABRIC tumors (P = 0.031). Interestingly, ER-, PR-, and HER2+ tumors showed significant preferential expression of the mutated allele in both datasets. Our work provides compelling evidence to support the clinical utility of PIK3CA allelic expression in breast cancer in identifying patients of poorer prognosis, and those with low expression of the mutated allele, who will unlikely benefit from PI3K inhibitors. Furthermore, our work proposes a model of differential regulation of a critical cancer-promoting gene in breast cancer.
- Over-elongation of centrioles in cancer promotes centriole amplification and chromosome missegregationPublication . Marteil, Gaelle; Guerrero, Adan; Vieira, Andre F.; de Almeida, Bernardo P.; Machado, Pedro; Mendonca, Susana; Mesquita, Marta; Villarreal, Beth; Fonseca, Irina; Francia, Maria E.; Dores, Katharina; Martins, Nuno P.; Jana, Swadhin C.; Tranfield, Erin M.; Barbosa-Morais, Nuno L.; Paredes, Joana; Pellman, David; Godinho, Susana A.; Bettencourt-Dias, MonicaCentrosomes are the major microtubule organising centres of animal cells. Deregulation in their number occurs in cancer and was shown to trigger tumorigenesis in mice. However, the incidence, consequence and origins of this abnormality are poorly understood. Here, we screened the NCI-60 panel of human cancer cell lines to systematically analyse centriole number and structure. Our screen shows that centriole amplification is widespread in cancer cell lines and highly prevalent in aggressive breast carcinomas. Moreover, we identify another recurrent feature of cancer cells: centriole size deregulation. Further experiments demonstrate that severe centriole over-elongation can promote amplification through both centriole fragmentation and ectopic procentriole formation. Furthermore, we show that overly long centrioles form over-active centrosomes that nucleate more microtubules, a known cause of invasiveness, and perturb chromosome segregation. Our screen establishes centriole amplification and size deregulation as recurrent features of cancer cells and identifies novel causes and consequences of those abnormalities.
- Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesisPublication . Braun, Simon; Enculescu, Mihaela; Setty, Samarth T.; Cortes-Lopez, Mariela; Almeida, Bernardo; Sutandy, F. X. Reymond; Schulz, Laura; Busch, Anke; Seiler, Markus; Ebersberger, Stefanie; Barbosa-Morais, Nuno L.; Legewie, Stefan; Konig, Julian; Zarnack, KathiMutations causing aberrant splicing are frequently implicated in human diseases including cancer. Here, we establish a high-throughput screen of randomly mutated minigenes to decode the cis-regulatory landscape that determines alternative splicing of exon 11 in the proto-oncogene MST1R (RON). Mathematical modelling of splicing kinetics enables us to identify more than 1000 mutations affecting RON exon 11 skipping, which corresponds to the pathological isoform RON Delta 165. Importantly, the effects correlate with RON alternative splicing in cancer patients bearing the same mutations. Moreover, we highlight heterogeneous nuclear ribonucleoprotein H (HNRNPH) as a key regulator of RON splicing in healthy tissues and cancer. Using iCLIP and synergy analysis, we pinpoint the functionally most relevant HNRNPH binding sites and demonstrate how cooperative HNRNPH binding facilitates a splicing switch of RON exon 11. Our results thereby offer insights into splicing regulation and the impact of mutations on alternative splicing in cancer.
- Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkersPublication . Almeida, Bernardo; Apolónio, Joana; Binnie, Alexandra; Castelo-Branco, PedroBackground Breast cancer is a highly heterogeneous disease resulting in diverse clinical behaviours and therapeutic responses. DNA methylation is a major epigenetic alteration that is commonly perturbed in cancers. The aim of this study is to characterize the relationship between DNA methylation and aberrant gene expression in breast cancer. Methods We analysed DNA methylation and gene expression profiles from breast cancer tissue and matched normal tissue in The Cancer Genome Atlas (TCGA). Genome-wide differential methylation analysis and methylation-gene expression correlation was performed. Gene expression changes were subsequently validated in the METABRIC dataset. The Oncoscore tool was used to identify genes that had previously been associated with cancer in the literature. A subset of genes that had not previously been studied in cancer was chosen for further analysis. Results We identified 368 CpGs that were differentially methylated between tumor and normal breast tissue (∆β > 0.4). Hypermethylated CpGs were overrepresented in tumor tissue and were found predominantly (56%) in upstream promoter regions. Conversely, hypomethylated CpG sites were found primarily in the gene body (66%). Expression analysis revealed that 209 of the differentially-methylated CpGs were located in 169 genes that were differently expressed between normal and breast tumor tissue. Methylation-expression correlations were predominantly negative (70%) for promoter CpG sites and positive (74%) for gene body CpG sites. Among these differentially-methylated and differentially-expressed genes, we identified 7 that had not previously been studied in any form of cancer. Three of these, TDRD10, PRAC2 and TMEM132C, contained CpG sites that showed diagnostic and prognostic value in breast cancer, particularly in estrogen-receptor (ER)-positive samples. A pan-cancer analysis confirmed differential expression of these genes together with diagnostic and prognostic value of their respective CpG sites in multiple cancer types. Conclusion We have identified 368 DNA methylation changes that characterize breast cancer tumor tissue, of which 209 are associated with genes that are differentially-expressed in the same samples. Novel DNA methylation markers were identified, of which cg12374721 (PRAC2), cg18081940 (TDRD10) and cg04475027 (TMEM132C) show promise as diagnostic and prognostic markers in breast cancer as well as other cancer types.