LncRNAs-associated to genomic instability: A barrier to cancer therapy effectiveness.

Although a large part of the genome is transcribed, only 1.9% has a protein-coding potential; most of the transcripts are non-coding RNAs such as snRNAs, tRNAs, and rRNAs that participate in mRNA processing and translation. In addition, there are small RNAs with a regulatory role, such as siRNAs, miRNAs, and piRNAs. Finally, the long non-coding RNAs (lncRNAs) are transcripts of more than 200 bp that can positively and negatively regulate gene expression (both in cis and trans), serve as a scaffold for protein recruitment, and control nuclear architecture, among other functions. An essential process regulated by lncRNAs is genome stability. LncRNAs regulate genes associated with DNA repair and chromosome segregation; they are also directly involved in the maintenance of telomeres and have recently been associated with the activity of the centromeres. In cancer, many alterations in lncRNAs have been found to promote genomic instability, which is a hallmark of cancer and is associated with resistance to chemotherapy. In this review, we analyze the most recent findings of lncRNA alterations in cancer, their relevance in genomic instability, and their impact on the resistance of tumor cells to anticancer therapy.

Methylation of Subtelomeric Chromatin Modifies the Expression of the lncRNA TERRA, Disturbing Telomere Homeostasis.

The long noncoding RNA (lncRNA) telomeric repeat-containing RNA (TERRA) has been associated with telomeric homeostasis, telomerase recruitment, and the process of chromosome healing; nevertheless, the impact of this association has not been investigated during the carcinogenic process. Determining whether changes in TERRA expression are a cause or a consequence of cell transformation is a complex task because studies are usually carried out using either cancerous cells or tumor samples. To determine the role of this lncRNA in cellular aging and chromosome healing, we evaluated telomeric integrity and TERRA expression during the establishment of a clone of untransformed myeloid cells. We found that reduced expression of TERRA disturbed the telomeric homeostasis of certain loci, but the expression of the lncRNA was affected only when the methylation of subtelomeric bivalent chromatin domains was compromised. We conclude that the disruption in TERRA homeostasis is a consequence of cellular transformation and that changes in its expression profile can lead to telomeric and genomic instability.

Proteasome inhibition alters mitotic progression through the upregulation of centromeric α-Satellite RNAs.

Cell cycle progression requires control of the abundance of several proteins and RNAs over space and time to properly transit from one phase to the next and to ensure faithful genomic inheritance in daughter cells. The proteasome, the main protein degradation system of the cell, facilitates the establishment of a proteome specific to each phase of the cell cycle. Its activity also strongly influences transcription. Here, we detected the upregulation of repetitive RNAs upon proteasome inhibition in human cancer cells using RNA-seq. The effect of proteasome inhibition on centromeres was remarkable, especially on α-Satellite RNAs. We showed that α-Satellite RNAs fluctuate along the cell cycle and interact with members of the cohesin ring, suggesting that these transcripts may take part in the regulation of mitotic progression. Next, we forced exogenous overexpression and used gapmer oligonucleotide targeting to demonstrate that α-Sat RNAs have regulatory roles in mitosis. Finally, we explored the transcriptional regulation of α-Satellite DNA. Through in silico analyses, we detected the presence of CCAAT transcription factor-binding motifs within α-Satellite centromeric arrays. Using high-resolution three-dimensional immuno-FISH and ChIP-qPCR, we showed an association between the α-Satellite upregulation and the recruitment of the transcription factor NFY-A to the centromere upon MG132-induced proteasome inhibition. Together, our results show that the proteasome controls α-Satellite RNAs associated with the regulation of mitosis.

Large-scale topological disruption of chromosome territories 9 and 22 is associated with nonresponse to treatment in CML.

Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm defined by the presence of t(9;22) translocation whose origin has been associated with the tridimensional genome organization. This rearrangement leads to the fusion of BCR and ABL1 genes giving rise to a chimeric protein with constitutive kinase activity. Imatinib, a tyrosine kinase inhibitor (TKI), is used as a first-line treatment for CML, though ~40% of CML patients do not respond. Here, using structured illumination microscopy (SIM) and 3D reconstruction, we studied the 3D organization patterns of the ABL1 and BCR genes, and their chromosome territories (CTs) CT9 and CT22, in CD34+ cells from CML patients that responded or not to TKI. We found that TKI resistance in CML is associated with high levels of structural disruption of CT9 and CT22 in CD34+ cells, increased CT volumes (especially for CT22), intermingling between CT9 and CT22, and an open-chromatin epigenetic mark in CT22. Altogether our results suggest that large-scale disruption of CT9 and CT22 correlates with the clinical response of CML patients, which could be translated into a potential prognostic marker of response to treatment in this disease and provide novel insights into the mechanisms underlying resistance to TKI in CML.

Genotoxicity of Marijuana in Mono-Users.

Marijuana (Cannabis sp.) is among the most recurred controlled substances in the world, and there is a growing tendency to legalize its possession and use; however, the genotoxic effects of marijuana remain under debate. A clear definition of marijuana's genotoxic effects remains obscure by the simultaneous consumption of tobacco and other recreational substances. In order to assess the genotoxic effects of marijuana and to prevent the bias caused by the use of substances other than cannabis, we recruited marijuana users that were sub-divided into three categories: (1) users of marijuana-only (M), (2) users of marijuana and tobacco (M+T), and (3) users of marijuana plus other recreative substances or illicit drugs (M+O), all the groups were compared against a non-user control group. We quantified DNA damage by detection of γH2AX levels and quantification of micronuclei (MN), one of the best-established methods for measuring chromosomal DNA damage. We found increased levels of γH2AX in peripheral blood lymphocytes from the M and M+T groups, and increased levels of MNs in cultures from M+T group. Our results suggest a DNA damage increment for M and M+T groups but the extent of chromosomal damage (revealed here by the presence of MNs and NBuds) might be related to the compounds found in tobacco. We also observed an elevated nuclear division index in all marijuana users in comparison to the control group suggesting a cytostatic dysregulation caused by cannabis use. Our study is the first in Mexico to assess the genotoxicity of marijuana in mono-users and in combination with other illicit drugs.

Differential response of immobile (pneumocytes) and mobile (monocytes) barriers against 2 types of metal oxide nanoparticles.

BACKGROUND: Inhaled nanoparticles (NPs) challenges mobile and immobile barriers in the respiratory tract, which can be represented by type II pneumocytes (immobile) and monocytes (mobile) but what is more important for biological effects, the cell linage, or the type of nanoparticle? Here, we addressed these questions and we demonstrated that the type of NPs exerts a higher influence on biological effects, but cell linages also respond differently against similar type of NPs. DESIGN: Type II pneumocytes and monocytes were exposed to tin dioxide (SnO2) NPs and titanium dioxide (TiO2) NPs (1, 10 and 50 µg/cm2) for 24 h and cell viability, ultrastructure, cell granularity, molecular spectra of lipids, proteins and nucleic acids and cytoskeleton architecture were evaluated. RESULTS: SnO2 NPs and TiO2 NPs are metal oxides with similar physicochemical properties. However, in the absence of cytotoxicity, SnO2 NPs uptake was low in monocytes and higher in type II pneumocytes, while TiO2 NPs were highly internalized by both types of cells. Monocytes exposed to both types of NPs displayed higher number of alterations in the molecular patterns of proteins and nuclei acids analyzed by Fourier-transform infrared spectroscopy (FTIR) than type II pneumocytes. In addition, cells exposed to TiO2 NPs showed more displacements in FTIR spectra of biomolecules than cells exposed to SnO2 NPs. Regarding cell architecture, microtubules were stable in type II pneumocytes exposed to both types of NPs but actin filaments displayed a higher number of alterations in type II pneumocytes and monocytes exposed to SnO2 NPs and TiO2 NPs. NPs exposure induced the formation of large vacuoles only in monocytes, which were not seen in type II pneumocytes. CONCLUSIONS: Most of the cellular effects are influenced by the NPs exposure rather than by the cell type. However, mobile, and immobile barriers in the respiratory tract displayed differential response against SnO2 NPs and TiO2 NPs in absence of cytotoxicity, in which monocytes were more susceptible than type II pneumocytes to NPs exposure.

Aging: Some theories, genetic, epigenetic and environmental considerations / Envejecimiento: algunas teorías y consideraciones genéticas, epigenéticas y ambientales

In this review several characteristics of the aging process are described and some theories that try to explain it are briefly mentioned. Although none of them fully explains this phenomenon, they can interact between each other in a complex way, out of which cellular senescence is the common outcome. Molecular changes take place on both genetic and epigenetic levels, and several studies have associated senescence with changes in the epigenetic-mediated chromatin condensation, while others consider that free radicals represent a useful mechanism to explain aging and age-related disorders that, along with the alteration of mitochondrial homeostasis, promote the aging process through the accumulation of damage along time.

En esta revisión se describen varias características del proceso de envejecimiento y de manera resumida algunas de las teorías que intentan explicarlo y, si bien ninguna es totalmente satisfactoria, pueden actuar entre sí de una manera compleja; en ellas, la senescencia celular es el factor común. Las alteraciones moleculares se llevan a cabo tanto a nivel genético como epigenético y varios estudios asocian la senescencia con cambios en la condensación de la cromatina, los cuales están regulados por factores epigenéticos y otros; en esos estudios se considera que los radicales libres representan un mecanismo útil para explicar el envejecimiento y los trastornos relacionados con la edad y que en forma conjunta, con las alteraciones en la homeostasis de la mitocondria, promueven el envejecimiento por daño acumulado a través del tiempo.

The use of long non-coding RNAs as prognostic biomarkers and therapeutic targets in prostate cancer.

Prostate cancer is the most common cancer in men and the second leading cause of cancer-related deaths. The most used biomarker to detect prostate cancer is Prostate Specific Antigen (PSA), whose levels are measured in serum. However, it has been recently established that molecular markers of cancer should not be based solely on genes and proteins but should also reflect other genomic traits; long non-coding RNAs (lncRNAs) serve this purpose. lncRNAs are transcripts of >200 bases that do not encode proteins and that have been shown to display abnormal expression profiles in different types of cancer. Experimental studies have highlighted lncRNAs as potential biomarkers for prognoses and treatments in patients with different types of cancer, including prostate cancer, where the PCA3 lncRNA is currently used as a diagnostic tool and management strategy. With the development of genomic technologies, particularly next-generation sequencing (NGS), several other lncRNAs have been linked to prostate cancer and are currently under validation for their medical use. In this review, we will discuss different strategies for the discovery of novel lncRNAs that can be evaluated as prognostic biomarkers, the clinical impact of these lncRNAs and how lncRNAs can be used as potential therapeutic targets.

Regulated expression of the lncRNA TERRA and its impact on telomere biology.

The telomere protects against genomic instability by minimizing the accelerated end resection of the genetic material, a phenomenon that results in severe chromosome instability that could favor the transformation of a cell by enabling the emergence of tumor-promoting mutations. Some mechanisms that avoid this fate, such as capping and loop formation, have been very well characterized; however, telomeric non-coding transcripts, such as long non-coding RNAs (lncRNAs), should also be considered in this context because they play roles in the organization of telomere dynamics, involving processes such as replication, degradation, extension, and heterochromatin stabilization. Although the mechanism through which the expression of telomeric transcripts regulates telomere dynamics is not yet clear, a non-coding RNA component opens the research options in telomere biology and the impact that it can have on telomere-associated diseases such as cancer.

[The role and importance of the microRNAs in the diagnosis and development of diseases]. / Importancia de los microARN en el diagnóstico y desarrollo de enfermedades.

MicroRNAs are small non-coding ribonucleic acids of endogenous nature. They persist in various groups of eukaryotes and perform critical functions during the development and the cell homeostasis. They have from 19 to 25 nucleotides in length and regulate the translation of the target RNA messenger (mRNA). MicroRNAs can inhibit its translation, stabilizing it or inducing its degradation. They regulate the genetic expression and are involved in the control of cellular functions (the differentiation, the proliferation, the apoptosis and the metabolism). They are also involved in the response to stress, the angiogenesis, the oncogenesis and in cardiovascular functions. That is the reason why their abnormal expressions are associated to many pathological conditions. The aim of this review was to describe the importance of microRNAs, their biological origin and their role in various diseases, such as cancer, diabetes, obesity, and neurological disorders. The microRNAs are an attractive therapeutic target because it has been observed that just one of them can regulate several genes and it could influence all the signaling route; besides, they could inhibit themselves in vivo without adverse effects related to the usual therapeutic agents. Since they can be detected in serum, plasma, urine and saliva samples in a stable, reproducible and consistent form between individuals of the same species, we expect them to be useful as biomarkers for the clinical diagnosis and the monitoring of diseases.

Los microARN son ácidos ribonucleicos pequeños no codificantes, endógenos, que se encuentran conservados en varios grupos de eucariontes y que desempeñan funciones críticas durante el desarrollo y la homeostasis celular. Son secuencias de una longitud entre 19 y 25 nucleótidos, que regulan la traducción de un ARN mensajero (ARNm) blanco, que inhiben su traducción, estabilizándolo o llevándolo a su degradación. Los microARN son reguladores de la expresión génica y participan en el control de procesos celulares como la diferenciación, la proliferación, la apoptosis y el metabolismo; también están involucrados en la respuesta al estrés, en la angiogénesis, la oncogénesis y los procesos cardiovasculares. De ahí que su desregulación o expresión anormal esté relacionada con numerosas condiciones patológicas. Esta revisión describe la importancia de los microARN, su biogénesis y su participación en enfermedades como cáncer, diabetes, obesidad y trastornos neurológicos. Los microARN representan un atractivo blanco terapéutico porque se ha observado que uno solo puede regular a muchos genes blanco e influir en toda la vía de señalización; además, pueden inhibirse in vivo sin muchos de los efectos adversos relacionados con los agentes terapéuticos tradicionales. Dado que se pueden detectar en suero, plasma, orina y saliva en forma estable, reproducible y consistente entre individuos de la misma especie, se espera que puedan utilizarse como biomarcadores para el diagnóstico clínico y monitoreo de enfermedades.

[Epigenetics, environment and asthma]. / Epigenética, medio ambiente y asma.

Asthma is a chronic inflammatory disease of the respiratory tract with a complex genetic background influenced by the exposition to a series of environmental factors. Genetic studies can only elucidate part of the heritability and susceptibility of asthma and even though several diseases have an evident genetic etiology, only a fraction of the genes involved in their pathogenicity have been identified. The epigenetic regulation of the latter is a fact one should bear in mind in order to explain the major triggers of diseases whose understanding is complicated, such as allergies and asthma. External stimulus such as nourishment, stress, physical activity, atmospheric pollution, tobacco smoking and alcohol drinking can induce either gene silencing or gene expression. In this regard, epigenetics can explain how these environmental factors influence our genetic inheritance. There is growing evidence that backs-up the fact that DNA methylation, histone post-translational modification and microRNA expression are influenced by the environment. This helps explaining how several of the risk factors mentioned contribute to the development and inheritance of asthma. In this review, different environmental factors and their relation with the main epigenetic regulatory mechanisms will be analyzed, as well as their possible role in the development of asthma.

El asma es una enfermedad inflamatoria crónica que afecta las vías respiratorias y tiene un componente genético complejo, que está mediada por la exposición a una variedad de desencadenantes ambientales. Los estudios genéticos no aclaran en su totalidad la herencia y susceptibilidad al asma. Muchas enfermedades son de origen genético; sin embargo, sólo se ha encontrado una fracción de los genes que las explican. La epigenética puede utilizarse para esclarecer las causas principales de padecimientos que son difíciles de entender, como la alergia y el asma. Estímulos externos como la nutrición, el estrés, la actividad física, la contaminación atmosférica y el consumo de tabaco y alcohol pueden silenciar o activar los genes. Al respecto, la epigenética ofrece explicaciones de cómo estos factores modifican sutilmente la herencia. Cada vez hay más evidencias que demuestran que los marcadores epigenéticos reconocidos, como la metilación del ADN, la modificación de histonas y la expresión de microRNAs están influidos por el ambiente. Esto ayuda a entender cómo muchos factores de riesgo similares a los señalados contribuyen a la aparición y herencia del asma. En esta revisión se analizan diferentes factores ambientales y su relación con los principales mecanismos epigenéticos, así como su posible influencia en la aparición del asma.