3D chromatin architecture and epigenetic regulation in cancer stem cells

Dedifferentiation of cell identity to a progenitor-like or stem cell-like state with increased cellular plasticity is frequently observed in cancer formation. During this process, a subpopulation of cells in tumours acquires a stem cell-like state partially resembling to naturally occurring pluripotent stem cells that are temporarily present during early embryogenesis. Such characteristics allow these cancer stem cells (CSCs) to give rise to the whole tumour with its entire cellular heterogeneity and thereby support metastases formation while being resistant to current cancer therapeutics. Cancer development and progression are demarcated by transcriptional dysregulation. In this article, we explore the epigenetic mechanisms shaping gene expression during tumorigenesis and cancer stem cell formation, with an emphasis on 3D chromatin architecture. Comparing the pluripotent stem cell state and epigenetic reprogramming to dedifferentiation in cellular transformation provides intriguing insight to chromatin dynamics. We suggest that the 3D chromatin architecture could be used as a target for re-sensitizing cancer stem cells to therapeutics.

Estudio genómico de la región crítica del cromosoma 21 asociada con el síndrome de Down / Genomic study of the critical region of chromosome 21 associated to Down syndrome

Introduction: Previous reports have identified a region of chromosome 21 known as Down syndrome critical region (DSCR) in which the expression of some genes would modulate the main clinical characteristics of this pathology. In this sense, there is currently limited information on the architecture of the DSCR associated. Objective: To obtain in silico a detailed vision of the chromatin structure associated with the evaluation of genomic covariables contained in public data bases. Methods: Taking as reference the information consigned in the National Center for Biotechnology Information, the Genome Browser from the University of California at Santa Cruz and from the HapMap project, a chromosome walk along 21 Mb of the distal portion of chromosome 21q arm was performed. In this distal portion, the number of single nucleotide polymorphisms (SNP), number of CpG islands, repetitive elements, recombination frequencies, and topographical state of that chromatin were recorded. Results: The frequency of CpG islands and Ref genes increased in the more distal 1.2 Mb DSCR that contrast with those localized near to the centromere. The highest level of recombination calculated for women was registered in the 21q22.12 to 22.3 bands. DSCR 6 and 9 genes showed a high percentage of methylation in CpG islands in DNA from normal and trisomic fibroblasts. The DSCR2 gene exhibited high levels of open chromatin and also methylation in some lysine residues of the histone H3 as relevant characteristics. Conclusion: The existence of a genomic environment characterized by high values of recombination frequencies and CpG methylation in DSCR 6 and 9 and also DSCR2 genes led us to postulate that in non-disjunction detected in Down syndrome, complex genomic, epigenetic and environmental relationships regulate some processes of meiosis.

Introducción: Análisis previos han identificado una región del cromosoma 21, conocida como región crítica del síndrome de Down (DSCR) en donde se localizan algunos genes cuya expresión modularía las principales características clínicas de este síndrome. En este sentido, existe poca información detallada sobre la arquitectura de la cromatina asociada con la DSCR. Objetivo: Obtener in silico, a partir de la evaluación de covariables genómicas contenidas en bases de datos públicas, una visión detallada de la estructura cromatina asociada con la DSCR. Métodos: Tomando como referencia la información consignada en el National Center for Biotechnology Information, el Genome Browser de la Universidad de California en Santa Clara y el proyecto internacional HapMap, se efectuó un paseo cromosómico a lo largo de 21Mb de la porción distal del brazo q del cromosoma 21, para registrar el número de polimorfismos de nucleótido único, el de islas CpG, de secuencias repetidas, las tasas de recombinación y el estado topológico de la cromatina asociada. Resultados: La frecuencia de islas CpG y de genes referenciados se incrementó en los últimos 1,2 Mb de la región distal en contraste con su distribución pericentromérica. La mayor tasa de recombinación calculada en este estudio para mujeres se registró en las bandas 21q22.13 y 21q22.3. Los genes DSCR 6 y 9 presentaron un elevado grado de metilación en islas CpG tanto en fibroblastos normales como en trisómicos. En el gen DSCR2 se observó un alto grado de descondensación cromatínica, además de metilación de diferentes residuos de lisina de la histona H3. Conclusiones: La existencia de un ambiente genómico caracterizado por tener elevadas tasas de recombinación y de metilación de genes DSCR 6 y 9, permite postular que en la no disyunción asociada con el SD, operarían complejas interacciones genómicas, epigenéticas y ambientales que actuarían en algunos procesos meióticos.