RESUMEN
Chromosomal instability is a hallmark of colorectal carcinogenesis and produces an accumulation of different forms of aneuploidies or broad copy number aberrations. Colorectal cancer is characterized by gain-type broad copy number aberrations, specifically in Chr20, Chr8q, Chr13 and Chr7, but their roles and mechanisms in cancer progression are not fully understood. It has been suggested that broad copy number gains might contribute to tumor development through the so-called caricature transcriptomic effect. We intend to investigate the impact of broad copy number gains on long non-coding RNAs' expression in colorectal cancer, given their well-known role in oncogenesis. The influence of such chromosomal aberrations on lncRNAs' transcriptome profile was investigated by SNP and transcriptome arrays in our series of colorectal cancer samples and cell lines. The correlation between aneuploidies and transcriptomic profiles led us to obtain a class of Over-UpT lncRNAs, which are transcripts upregulated in CRC and further overexpressed in colon tumors bearing specific chromosomal aberrations. The identified lncRNAs can contribute to a wide interaction network to establish the cancer driving effect of gain-type aneuploidies.
Asunto(s)
Aneuploidia , Neoplasias Colorrectales , Regulación Neoplásica de la Expresión Génica , ARN Largo no Codificante , Humanos , ARN Largo no Codificante/genética , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/patología , Variaciones en el Número de Copia de ADN , Transcriptoma , Femenino , Línea Celular Tumoral , Perfilación de la Expresión Génica , Masculino , Inestabilidad Cromosómica , Persona de Mediana Edad , Aberraciones Cromosómicas , Polimorfismo de Nucleótido SimpleRESUMEN
Cyclin-dependent Kinase 2 (CDK2) inhibition prevents supernumerary centrosome clustering. This causes multipolarity, anaphase catastrophe and apoptotic death of aneuploid cancers. This study elucidated how CDK2 antagonism affected centrosome stoichiometry. Focused ion beam scanning electron microscopy (FIB-SEM) and immunofluorescent imaging were used. Studies interrogated multipolar mitosis after pharmacologic or genetic repression of CDK2. CDK2/9 antagonism with CYC065 (Fadraciclib)-treatment disordered centrosome stoichiometry in aneuploid cancer cells, preventing centrosome clustering. This caused ring-like chromosomes or multipolar cancer cells to form before onset of cell death. Intriguingly, CDK2 inhibition caused a statistically significant increase in single centrioles rather than intact centrosomes with two centrioles in cancer cells having chromosome rings or multipolarity. Statistically significant alterations in centrosome stoichiometry were undetected in other mitotic cancer cells. To confirm this pharmacodynamic effect, CDK2 but not CDK9 siRNA-mediated knockdown augmented cancer cells with chromosome ring or multipolarity formation. Notably, engineered gain of CDK2, but not CDK9 expression, reversed emergence of cancer cells with chromosome rings or multipolarity, despite CYC065-treatment. In marked contrast, CDK2 inhibition of primary human alveolar epithelial cells did not confer statistically significant increases of cells with ring-like chromosomes or multipolarity. Hence, CDK2 antagonism caused differential effects in malignant versus normal alveolar epithelial cells. Translational relevance was confirmed by CYC065-treatment of syngeneic lung cancers in mice. Mitotic figures in tumors exhibited chromosome rings or multipolarity. Thus, CDK2 inhibition preferentially disorders centrosome stoichiometry in cancer cells. Engaging this disruption is a strategy to explore against aneuploid cancers in future clinical trials.
Asunto(s)
Centrosoma , Neoplasias , Humanos , Animales , Ratones , Quinasa 2 Dependiente de la Ciclina/genética , Quinasa 2 Dependiente de la Ciclina/metabolismo , Centrosoma/metabolismo , Anafase , Mitosis/genética , Aneuploidia , Neoplasias/genética , Neoplasias/metabolismoRESUMEN
Derivative chromosome der(1;16), isochromosome 1q, and deleted 16q-producing arm-level 1q-gain and/or 16q-loss-are recurrent cytogenetic abnormalities in breast cancer, but their exact role in determining the malignant phenotype is still largely unknown. We exploited The Cancer Genome Atlas (TCGA) data to generate and analyze groups of breast invasive carcinomas, called 1,16-chromogroups, that are characterized by a pattern of arm-level somatic copy number aberrations congruent with known cytogenetic aberrations of chromosome 1 and 16. Substantial differences were found among 1,16-chromogroups in terms of other chromosomal aberrations, aneuploidy scores, transcriptomic data, single-point mutations, histotypes, and molecular subtypes. Breast cancers with a co-occurrence of 1q-gain and 16q-loss can be distinguished in a "low aneuploidy score" group, congruent to der(1;16), and a "high aneuploidy score" group, congruent to the co-occurrence of isochromosome 1q and deleted 16q. Another three groups are formed by cancers showing separately 1q-gain or 16q-loss or no aberrations of 1q and 16q. Transcriptome comparisons among the 1,16-chromogroups, integrated with functional pathway analysis, suggested the cooperation of overexpressed 1q genes and underexpressed 16q genes in the genesis of both ductal and lobular carcinomas, thus highlighting the putative role of genes encoding gamma-secretase subunits (APH1A, PSEN2, and NCSTN) and Wnt enhanceosome components (BCL9 and PYGO2) in 1q, and the glycoprotein E-cadherin (CDH1), the E3 ubiquitin-protein ligase WWP2, the deubiquitinating enzyme CYLD, and the transcription factor CBFB in 16q. The analysis of 1,16-chromogroups is a strategy with far-reaching implications for the selection of cancer cell models and novel experimental therapies.
RESUMEN
Somatic copy number alterations (SCNAs) serve as hallmarks of tumorigenesis and often result in deviations from one-to-one allelic ratios at heterozygous loci, leading to allelic imbalance (AI). The Cancer Genome Atlas (TCGA) reports SCNAs identified using a circular binary segmentation algorithm, providing segment mean copy number estimates from single-nucleotide polymorphism DNA microarray total intensities (log R ratio), but not allele-specific intensities ("B allele" frequencies) that inform of AI. Our approach provides more sensitive identification of SCNAs by modeling the "B allele" frequencies jointly, thereby bolstering the catalog of chromosomal alterations in this widely utilized resource. Here we present AI summaries for all 33 tumor sites in TCGA, including those induced by SCNAs and copy-neutral loss-of-heterozygosity (cnLOH). We identified AI in 94% of the tumors, higher than in previous reports. Recurrent events included deletions of 17p, 9q, 3p, amplifications of 8q, 1q, 7p, as well as mixed event types on 8p and 13q. We also observed both site-specific and pan-cancer (spanning 17p) cnLOH, patterns which have not been comprehensively characterized. The identification of such cnLOH events elucidates tumor suppressors and multi-hit pathways to carcinogenesis. We also contrast the landscapes inferred from AI- and total intensity-derived SCNAs and propose an automated procedure to improve and adjust SCNAs in TCGA for cases where high levels of aneuploidy obscured baseline intensity identification. Our findings support the exploration of additional methods for robust automated inference procedures and to aid empirical discoveries across TCGA.
Asunto(s)
Aberraciones Cromosómicas , Variaciones en el Número de Copia de ADN , Frecuencia de los Genes , Neoplasias/genética , Cromosomas Humanos/genética , Bases de Datos Genéticas , Humanos , Pérdida de Heterocigocidad , Neoplasias/clasificaciónRESUMEN
Anti-tumor immune responses impede tumor formation, and cancers have evolved many mechanisms of immune evasion. Confirming earlier findings, we show that human tumors with high chromosomal instability (CIN+) are significantly less immunogenic, as judged by tumor lymphocyte infiltration, compared to those with more stable genomes (CIN-). This finding is paradoxical, as genomic instability is expected to evoke an innate immune response. Importantly, CIN+ tumors and cell lines exhibited suppressed expression of proteins involved in MHC class I antigen presentation at least partly due to DNA hypermethylation of the corresponding genes. Using a mouse model of the in vivo evolution of aneuploid tumors, we found that the induction of chromosomal instability in tumor cells is highly immunogenic due to the activation of the STING/TBK1 pathway and consequent increased interferon signaling and antigen presentation. However, tumors evolving under immune pressure suppress the STING/TBK1 and antigen presentation pathways and evade anti-tumor immune responses. In contrast, CIN+ tumors that develop under low immune pressure in both humans and mice retain efficient MHC class I antigen presentation and immunogenicity. Altogether, this study identifies an important mechanism of immune evasion in chromosomally unstable tumors.
RESUMEN
Broad Copy Number Gains (BCNGs) are copy-number increases of chromosomes or large segments of chromosomal arms. Publicly-available single-nucleotide polymorphism (SNP) array and RNA-Seq data of colon adenocarcinoma (COAD) samples from The Cancer Genome Atlas (TCGA) consortium allowed us to design better control groups in order to identify changes in expression due to highly recurrent BCNGs (in chromosomes 20, 8, 7, 13). We identified: (1) Overexpressed Transcripts (OverT), transcripts whose expression increases in "COAD groups bearing a specific BCNG" in comparison to "control COAD groups" not bearing it, and (2) up-regulated/down-regulated transcripts, transcripts whose expression increases/decreases in COAD groups in comparison to normal colon tissue. An analysis of gene expression reveals a correlation between the density of up-regulated genes per selected chromosome and the recurrence rate of their BCNGs. We report an enrichment of gained enhancer activity and of cancer fitness genes among OverT genes. These results support the hypothesis that the chromosomal density of overexpressed cancer fitness genes might play a significant role in the selection of gained chromosomes during cancer evolution. Analysis of functional pathways associated with OverT suggest that some multi-subunit protein complexes (eIF2, eIF3, CSTF and CPSF) are candidate targets for silencing transcriptional therapy.
Asunto(s)
Adenocarcinoma , Cromosomas Humanos/metabolismo , Neoplasias del Colon , Elementos de Facilitación Genéticos , Dosificación de Gen , Regulación Neoplásica de la Expresión Génica , Genes Relacionados con las Neoplasias , Modelos Biológicos , Proteínas de Neoplasias , Regulación hacia Arriba , Adenocarcinoma/genética , Adenocarcinoma/metabolismo , Adenocarcinoma/patología , Cromosomas Humanos/genética , Neoplasias del Colon/genética , Neoplasias del Colon/metabolismo , Neoplasias del Colon/patología , Humanos , Proteínas de Neoplasias/biosíntesis , Proteínas de Neoplasias/genéticaRESUMEN
Triple-negative breast cancer (TNBC) is an aggressive subtype that frequently develops resistance to chemotherapy. An unresolved question is whether resistance is caused by the selection of rare pre-existing clones or alternatively through the acquisition of new genomic aberrations. To investigate this question, we applied single-cell DNA and RNA sequencing in addition to bulk exome sequencing to profile longitudinal samples from 20 TNBC patients during neoadjuvant chemotherapy (NAC). Deep-exome sequencing identified 10 patients in which NAC led to clonal extinction and 10 patients in which clones persisted after treatment. In 8 patients, we performed a more detailed study using single-cell DNA sequencing to analyze 900 cells and single-cell RNA sequencing to analyze 6,862 cells. Our data showed that resistant genotypes were pre-existing and adaptively selected by NAC, while transcriptional profiles were acquired by reprogramming in response to chemotherapy in TNBC patients.
Asunto(s)
Antineoplásicos/uso terapéutico , Resistencia a Antineoplásicos/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Neoplasias de la Mama Triple Negativas/tratamiento farmacológico , Estudios de Casos y Controles , Análisis por Conglomerados , Variaciones en el Número de Copia de ADN , Exoma/genética , Femenino , Frecuencia de los Genes , Genotipo , Humanos , Terapia Neoadyuvante , Análisis de Secuencia de ADN , Análisis de Secuencia de ARN , Análisis de la Célula Individual , Análisis de Supervivencia , Transcriptoma , Neoplasias de la Mama Triple Negativas/metabolismo , Neoplasias de la Mama Triple Negativas/mortalidad , Neoplasias de la Mama Triple Negativas/patologíaRESUMEN
el diagnóstico y tamizaje prenatal, así como el diagnóstico y seguimiento de enfermedades en diversos campos de la medicina, se hace, en la actualidad, de manera más sencilla gracias al ADN libre en plasma. Este ADN representa una pequeña parte de la información genética de un tejido en particular o, en el caso de las mujeres en embarazo, una proporción del ADN fetal. En la oncología, por ejemplo, dada la heterogeneidad del cáncer, la aplicación del ADN libre en plasma ha sido difícil de implementar ya que solo existen algunos biomarcadores tumorales específicos para su uso en investigación. Metodologías como la reacción en cadena de la polimerasa (PCR) en tiempo real muestran una gran sensibilidad para detectar mutaciones que permitan establecer un correcto dignóstico y tratamiento de algunas enfermedades como las fetales o las tumorales, al mismo tiempo que disminuye costos. Lo anterior, no deja de ser una gran oportunidad para continuar los procesos de investigación y desarrollo de pruebas que permitan, en un futuro cercano, implementar el uso del ADN libre de células en el área clínica, con resultados confiables en el diagnóstico y tratamiento de enfermedades sin poner en riesgo la integridad del paciente
The prenatal diagnosis and screening, as well as the diagnosis and monitoring of diseases in various medicine fields, is now made more easily thanks to the cell free DNA present in plasma. This DNA represents a small part of the genetic information of a particular tissue or, in the case of pregnant women, a proportion of the fetal DNA. In oncology, for example, given the heterogeneity of cancer, the application of cell free DNA has been difficult to implement since there are only some specific tumoral biomarkers for research use. Methodologies such as real-time polymerase chain reaction (PCR) show a high sensitivity to detect mutations that allow a correct diagnosis and treatment of fetal or tumoral diseases, at the same time reducing costs. This represents a great opportunity to continue the research and developmental processes of tests that allow its implementation in the clinical area in the near future, with reliable results in diagnosis and treatment of diseases without compromising the patient's integrity