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CABD News



Identification of Conserved MEL-28/ELYS Domains with Essential Roles in Nuclear Assembly and Chromosome Segregation

                                        
Most animal cells have a nucleus that contains the genetic material: the chromosomes. The nucleus is enclosed by the nuclear envelope, which provides a physical barrier between the chromosomes and the surrounding cytoplasm and enables precisely controlled transport of proteins into and out of the nucleus. Transport occurs through nuclear pore complexes, which consist of multiple copies of ~30 different proteins called nucleoporins. Although the composition of nuclear pore complexes is known, the mechanisms of their assembly and function are still unclear.

We have analyzed the nucleoporin MEL-28/ELYS through a systematic dissection of functional domains both in the nematode Caenorhabditis elegans and in human cells. Interestingly, MEL-28/ELYS localizes not only to nuclear pore complexes, but is also associated with chromosomal structures known as kinetochores during cell division. Our studies have revealed that even small perturbations in MEL-28/ELYS can have dramatic consequences on nuclear pore complex assembly as well as on separation of chromosomes during cell division. Surprisingly, inhibition of MEL-28/ELYS causes cell-cycle delay, suggesting activation of a cellular surveillance system for chromosomal damages. Finally, we conclude that the structural domains of MEL-28/ELYS are conserved from nematodes to humans.

Georgina Gómez-Saldivar, Anita Fernandez, Yasuhiro Hirano, Michael Mauro, Allison Lai, Cristina Ayuso, Tokuko Haraguchi, Yasushi Hiraoka, Fabio Piano y Peter Askjaer. Identification of Conserved MEL-28/ELYS Domains with Essential Roles in Nuclear Assembly and Chromosome Segregation. PLOS Genetics. DOI: 10.1371/journal.pgen.1006131



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La aparición de apéndices en vertebrados fue posible por un cambio en la organización 3D del genoma
16/02/1016



El genoma es una cadena muy larga de ADN que tiene que plegarse en el espacio tridimensional de una forma muy precisa para poder ajustarse al tamaño del para  núcleo de las células. Recientemente se ha visto además que esa organización 3D del genoma es crítico para la correcta activación de los genes. Científicos del CSIC y de la Universidad Pablo de Olavide, en colaboración con un grupo Francés, han demostrado que la región del genoma que contiene los genes Hox, los cuales son esenciales para la formación de múltiples estructuras de los animales, ha sufrido un cambio en su estructura 3D en la transición de invertebrados a vertebrados que ha sido fundamental para el correcto desarrollo de las extremidades.

 

Todos los animales se construyen, en gran medida, con el mismo conjunto de genes. Lo que hace unos animales diferentes a otros es cuando, cuanto y donde se encienden esos genes. Esto de pende de regiones reguladoras que actúan como interruptores que encienden y apagan los genes. De hecho la cantidad de ADN que contiene genes es muy pequeña, entre el 2-5% del genoma. El resto alberga una ingente cantidad de dichos interruptores que controlan de forma muy precisa la activación de los todos genes en diferentes tejidos y órganos a lo largo de la vida de los animales. Estos interruptores se distribuyen en la vecindad genómica de los genes que controlan, ocupando a veces grandes regiones genómicas. El ADN lineal encontramos así un gen, muchas regiones reguladoras, otro gen, más regiones reguladoras, y así sucesivamente. ¿Como se organiza entonces el genoma para que las regiones reguladoras de un gen con enciendan o apaguen al gen vecino? Este problema se ha resuelto en la evolución generando compartimentos separados para cada gen y el conjunto de sus regiones reguladoras. Dichos compartimentos son similares a los ovillos que se forman en un hilo de lana. Un hilo de lana sería el ADN, que va formando pequeños ovillos ligados por un segmento que los conecta. Cada ovillo sería un territorio donde un gen tendría plegado en su proximidad sus interruptores, todo ello separado del siguiente bloque compuesto de otro gen con sus elementos reguladores, y así a lo largo de toda la cadena de ADN.

 

Los genes Hox son fundamentales para la construcción de todos los animales. Así, por ejemplo, se requieren para establecer el eje desde la cabeza a la cola y también para formar las extremidades. En el genoma están formando un complejo en los cuales los distintos genes se disponen en tándem, unos detrás de otro. A ambos lados del complejo Hox existe una amplia región genómica repleta de elementos reguladores necesarios para controlar la activación de estos genes de forma muy precisa. Para la correcta formación de las extremidades, es esencial que los elementos reguladores que están un lado del genoma solo enciendan los genes Hox de ese lado, mientras que los interruptores al lado contrario del complejo Hox, solo deben controlar a sus genes más cercanos. Puesto que los genes Hox están todos muy juntos, unos pegados a otros, en vertebrados, el complejo Hox esta partido en dos compartimentos (ovillos) diferentes, uno con los genes de un lado y todo los elementos reguladores localizados en ese lado del genoma, y otro similar en el otro lado del complejo.

 

El grupo del profesor Gómez Skarmeta del CSIC y la Universidad Pablo de Olavide (UPO), junto con el grupo de biología computacional del Dr. Damien Devos de la UPO y el grupo del Dr. Hector Escivá de la estación marina de Bayuls en Francia, han demostrado que dicha  organización 3D del complejo Hox es una innovación evolutiva de vertebrados. Mediante técnicas genómicas, ensayos de transgénesis en peces y modelos computacionales, este equipo ha demostrado que el complejo Hox de Amphioxus, un cefalocordado marino parecido a un gusano, que sin embargo es el animal invertebrado vivo más parecido al ancestro de todos los vertebrados, carece de esa división tridimensional en dos compartimentos. De hecho, el complejo Hox de dicho organismo esta organizado en un único compartimento que contiene todos los genes y una extensa región a un lado del genoma rica en elementos reguladoras. Esto nos ha permitido postular una hipótesis según la cual, en la transición entre invertebrados y vertebrados, la aparición de numerosas regiones reguladoras al otro lado del complejo tuvo lugar en paralelo con la partición del complejo en dos compartimentos, para evitar que dichas regiones nuevas afectaran a los genes del otro lado del complejo.

Nuestro trabajo evidencia la importancia de la co-evolución de información reguladora y organización tridimensional del genoma.

 

Es evidente que la alteración de esta subdivisión en compartimentos de la cromatina en dominios tridimensionales, en gran medida, puede ser fuente de graves patologías. De hecho, estudios recientes han demostrado como la fusión de dos compartimentos puede causar diferentes malformaciones al activarse determinados genes con interruptores de un compartimento vecino.

 

Después de conocer todos los genes humanos, toco identificar sus interruptores. Ahora toca estudiar en profundidad como se organiza en el espacio tridimensional toda esta información reguladora en el genoma. Por desgracia para nosotros, y beneficio de otros, cada uno de estos pasos de gigante en el conocimiento de como se construye un ser humano, la lectura del genoma, la identificación del epigenoma (regiones reguladoras) y ahora el estudio de estructura 3D del genoma, han estado y siguen estando liderados por otros gobiernos que reconocen estos problemas como importantes para el conocimiento y la salud humana. Mientras dichos gobiernos invierten cantidades importantes de dinero público y privado apostando por conocimiento del futuro, nosotros, con menguantes y limitados presupuesto en ciencia, y cada vez menos capital humano, no desfalleceremos e intentaremos seguir haciendo nuestras pequeñas aportaciones.

 

Rafael D Acemel, Juan J Tena, Ibai Irastorza, Ferdinand Marlétaz, Carlos Gómez-Marín, Elisa de la Calle-Mustienes, Stéphanie Bertrand, Sergio G Diaz, Daniel Aldea, Jean-Marc Aury, Sophie Mangenot, Peter W H Holland, Damien P Devos, Ignacio Maeso, Hector Escrivá & José Luis Gómez-Skarmeta. A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation. Nature Genetics. DOI: 10.1038/ng.3497

The Andalusian Centre for Developmental Biology (CABD) participates in a European network COST on autophagy
24/11/2015





The CABD participates in the European Network on Research and Knowledge Transfer Autophagy "TRANSAUTOPHAGY" led by professor and researcher Caty Casas Louzao member of the research group in Neuroplasticity and Regeneration Neurosciences Institute (INC) of the Autonomous University of Barcelona. From the CABD, the research group of José A. Sánchez Alcázar participates in the project.
The consortium will provide a platform to foster collaboration and exchange of knowledge between businesses, researchers from various disciplines (nanotechnologists, bioinformatics, physicists, chemists, biologists and physicians), and other related agents.
The project foresees biomedical advances in prevention, diagnostic and therapy in several pathologies such as cancer and neurodegeneration, as well as advances in the improvement of the living quality related with the diet or alternative sources of clean energy.
Autophagy is essential for the maintenance of homeostasis in cells and organisms. Autophagy controls the proper balance of nutrients and eliminates damaged or excess of elements inside the cell, altered proteins and even invasive microorganisms.
As for the health of people, autophagy is a mechanism of great therapeutic importance, with potential benefits to fight cancer, lupus erythematosus or neurodegeneration, among others. It has also been shown to be a key element in the fight against aging.
In the biotechnology field, modulation of autophagy showed applications for optimizing agricultural production and for alternative energy sources from microalgae.
The network potentiates the open innovation as a tool for creative resolution of problems, all offering opportunities for young researchers and taking care of the equality of gender issues.
It is main objective of the Consortium speed the translation of the knowledge generated in products and processes for their utilisation in the fields of the biomedicine and biotechnology.
The network also foresees the divulging and transfer of the results to the society that will go since recommendations for a healthy aging or for the prevention of illnesses, until the discovery of new therapies or the development of biocomponents or nanodevices to modulate the autophagy selectively. The results will be able to have clinical applications, as anticancer agents, or neuroprotectors, as well as applications with plants and microorganisms for crop efficiency and alternative sources of energy.
The COST (European Cooperation in Science and Technology) actions of the European Union foster the creation of international networks of research during four years.

CABD researchers have patented a new treatment for lysosomal diseases.
05/06/2015

The research group of José A. Sánchez Alcázar in collaboration with José Manuel Garcia Fernandez (CSIC) and Carmen Ortiz Mellet (University of Sevilla) has patented a new composition for the treatment of lysosomal diseases (P201530471/2015). Lysosomal storage disorders describe a heterogeneous group of inherited rare diseases with loss of function of lysosomal enzymes. As a result of abnormal enzyme activity various substrates are progressively accumulated in lysosomes and other organelles as mitochondria. The clinical phenotype includes visceromegaly, neurological and bone alterations, and premature death. Currently some of these diseases only have symptomatic therapy following two therapeutic approaches: substrate reduction therapy (SRT), which inhibits the enzymes involved in the production of accumulated substrates, and enzyme replacement therapy (ERT), consisting in the exogenous administration of the active recombinant enzymes that are defective in the patients. Gaucher disease is the most prevalent lysosomal disorder storage. It is caused by mutations in the gene GBA1 resulting in insufficient or defective β-glucocerebrosidase activity. The decrease of catalytic activity results in the accumulation of glucosylceramide and glucosyl sphingolipids in the lysosomes of macrophages and visceral organs. One of the most prevalent mutations in Gaucher disease is the L444P variant, resulting in incorrect folding in the ER and impaired transport to the lysosome. Patients homozygous for the L444P mutation have severe neurological forms of the disease. This mutation is particularly refractory to available treatments, including ERT, so there is an urgent need to develop therapeutic strategies for patients with this genotype. The present invention describes that the combination of a pharmacological chaperone and coenzyme Q10 (CoQ) in cellular models of Gaucher disease produces a higher benefit than individual treatments, representing an improved therapeutic option for the treatment of Gaucher disease, especially for the neuronopathic forms of the disease.



The research that originated the patent has been published in Scientific reports, 5:10903, 2015. Pharmacological Chaperones and Coenzyme Q10 Treatment Improves Mutant β-Glucocerebrosidase Activity and Mitochondrial Function in Neuronopathic Forms of Gaucher Disease.

¿Cómo se organiza la información en el genoma?
02/06/2015

¿Cómo se organiza la información en el genoma?
Esta se ha convertido en una pregunta clave para entender los genomas de los animales, y es el tema central de un nuevo proyecto a gran escala en EEUU denominado 4DNucleome. Cuando se culmino uno de los proyectos científicos mas importantes del siglo pasado, la secuenciación del genoma humano, se evidencio que conocer la secuencia lineal del genoma no nos ayudaba entender como funcionaba. De la lectura de dicha secuencia solo podíamos entender pequeños párrafos, no mas del 5%, que contenían la información necesaria para generar las proteínas, lo que se denomina ADN codificante o genes. ¿Que información había en la gran mayoría del resto del genoma?. El desconocimiento nos llevo a llamarlo ADN basura. Sin embargo, el trabajo de numerosos grupos de investigación, y sobre todo, de un nuevo proyecto a gran escala financiado por el gobierno de EEUU, el proyecto ENCODE, ha demostrado que es ese ADN No codificante, se encuentran todas las regiones reguladoras, instrucciones o interruptores, que encienden de una forma muy precisa, en el espacio y en el tiempo, los diferentes genes del genoma. Estos interruptores, activos o apagados en diferentes células, encienden unos u otros genes, generando los diferentes tejidos de un organismo. Es mas, puesto que la secuenciación de multitud de otros genomas de animales ha demostrado que los genes están altamente conservados en todos los vertebrados, hoy en día esta claro que lo que nos hace a los distintos vertebrados diferentes, en gran medida, es el conjunto especifico de regiones reguladoras que tenemos cada uno y que encienden de forma diferencial a los mismos genes en distintas especies. Aunque la mayoría de estas regiones reguladoras son diferentes en distintas especies, la comparación de los genomas de vertebrados revelo la existencia de un subconjunto de regiones comunes a todas las especies. Estas instrucciones son necesarias para activar a los mismos genes en los mismos momentos y lugares durante la embriogénesis, lo que permite generar el plan corporal común a todos los vertebrados. A partir de este punto de convergencia morfológica, que define un tipo de estructura animal, vertebrado en este caso, tiene lugar una mayor diferencia de expresión de genes entre distintas especies que genera las diferencias morfológicas que vemos entre diferentes animales.

¿Que más podemos aprender de la comparación de genomas?
En los últimos años, en estudios principalmente en mamíferos, se ha visto que la gran cantidad de información reguladora del genoma se organiza segmentos cromosómicos de unos 0.5-2 millones de pares de bases (Megabases) que forman especies de madejas donde distintas regiones interacciones frecuentemente unas con otras, permitiendo que los promotores de los genes puedan interaccionar con todas sus regiones reguladoras incluso a grandes distancias. Estas regiones se llaman TADs, acrónimo de Topological associating domains (dominios de asociación topológica). La interacción entre regiones genómicas de TADs vecinos es mínima, lo que permite aislar la información reguladora de cada TAD para que solo afecte al o los genes dentro de este y no los del TAD vecino, o lo que es los mismo, que los paisajes reguladores (lo que ve cada gen) sean diferentes para genes vecinos en el ADN lineal. En este trabajo hemos comparado como se organiza la información reguladora en esos TADs a lo largo de la evolución alrededor de los genes Six, unos genes que están asociados físicamente unos a otros en el ADN formando complejos génicos, que son esenciales para la construcción de todos los animales y que están afectados en mutaciones humanas. En nuestro estudio hemos visto que en no solo en vertebrados, sino también en erizo de mar, un animal con un origen evolutivo mas ancestral que los vertebrados, los complejos de genes Six están formados por dos TADs que permiten que las regiones reguladoras flanqueando a los genes Six a cada lado del complejo interaccionen específicamente con unos y no con otros genes. Por tanto, a lo largo de la evolución de los deuterostomos (el grupo que abarca, erizos y vertebrados) estos TADs han facilitado que los genes Six, muy próximos en el genoma, interacciones con grupos distintos de elementos reguladores y se enciendan, en el espacio y en el tiempo de forma muy diferente, o lo que es lo mismo, tengan paisajes reguladores diferentes, participando en la generación de diferentes órganos y tejidos. Además, hemos podido comprobar que cuando eliminamos la región del genoma que contiene la intersección entre los dos TADs, la información reguladora de un TAD afecta al gen del TAD vecino indicando que esta zona hace de barrera que divide el genoma en dos zonas reguladoras independientes. Por ultimo, mediante una comparación evolutiva las secuencias de esta zona donde esta la barrera entre los dos TADs, en humanos, ratón, peces y erizos, hemos visto que la proteína CTCF, que se une a ADN y permite la interacción física entre dos regiones del genoma distantes, posiblemente juega un papel fundamental, conservado evolutivamente, en el establecimiento de dichas barreras. Una vez más, la comparación evolutiva, en este caso de los paisajes reguladores de genes relevantes para la construcción de los animales , ha sido esencial para comprender como se organiza la cromatina en el espacio tridimensional del núcleo



Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders. Carlos Gómez-Marína, Juan J. Tena, Rafael D. Acemel, Macarena López-Mayorga, Silvia Naranjo, Elisa de la Calle-Mustienes, Ignacio Maeso, Leonardo Beccari, Ivy Aneas, Erika Vielmas, Paola Bovolenta, Marcelo A. Nobrega, Jaime Carvajal and José Luis Gómez-Skarmeta. PNAS June 1, 2015 DOI: 10.1073/pnas.1505463112




Identificado el epigenoma de las células precursoras de páncreas humano
27/04/2015

-Un estudio con participación del CABD identifica el epigenoma de las células precursoras de páncreas humanos

-Los hallazgos validados en organismos vivos usando peces cebra abren nuevas vías para el desarrollo de la medicina regenerativa

-Este trabajo potenciará el uso de células de páncreas generadas en el laboratorio a partir de células madre humanas





Un equipo internacional de investigadores con participación del Centro Andaluz de Biología del Desarrollo (CABD) ha identificado los interruptores del genoma que encienden a los genes necesarios para generar células precursoras de páncreas humanos. Este estudio, publicado en la revista Nature Cell Biology, permite identificar nuevas moléculas implicadas en la proliferación de estas células y abre nuevas vías para el desarrollo de la medicina regenerativa.

“El páncreas es un órgano productor de enzimas y hormonas con un papel esencial para la vida, ya que controla la digestión de los alimentos y los niveles de azúcar en sangre”, explica José Luis Gómez-Skarmeta, co-responsable del trabajo en el Centro Andaluz de Biología del Desarrollo (centro mixto del CSIC y la Universidad Pablo de Olavide, en Sevilla). Un fallo en el funcionamiento del páncreas puede causar enfermedades como la diabetes e incluso la muerte.

Por estos motivos, la regeneración del páncreas a partir de células madre es una línea de intensa investigación en la medicina regenerativa. “Sin embargo, para poder regenerar el páncreas hay que entender primero cómo se construye durante la embriogénesis”, indica Jorge Ferrer, uno de los responsables del trabajo e investigador del Imperial College de Londres y del Institut d’Investigacions Biomèdiques August Pi i Sunyer, de Barcelona.

A pesar de tener todas el mismo genoma, las diferentes células del organismo se generan mediante la activación específica en cada una de ellas de un determinado número de genes. “Esta activación depende de instrucciones distribuidas por el genoma que encienden o apagan los genes de forma selectiva en determinados tejidos y en momentos precisos del desarrollo embrionario, lo que se llama el epigenoma”, explica Gómez-Skarmeta.

“En este trabajo hemos identificado el epigenoma de las células precursoras de páncreas humanos, que son aquellas células que generarán todos los componentes celulares del páncreas. Además hemos comparado el epigenoma de células de páncreas de embriones humanos con el de células del mismo tipo generadas en el laboratorio a partir de células madre humanas, y hemos demostrado su gran parecido. Esto potenciará el uso de las células generadas en laboratorio en estudios futuros, comenta Ferrer.

“Además, el estudio de dichas instrucciones nos han permitido demostrar que la vía de Hippo, una vía de señalización celular implicada en el control del tamaño de los órganos, y que cuando se desregula provoca varios tipos de cáncer, es esencial para el correcto crecimiento de los precursores pancreáticos”, añade Ferrer.

“El uso de pez cebra nos ha permitido demostrar que las instrucciones identificadas actúan realmente como interruptores que encienden los genes en el páncreas, además de permitirnos observar en un animal modelo el impacto de reducir la actividad de la vía Hippo en el desarrollo del páncreas”, señala Gómez-Skarmeta.

“Este estudio será de gran utilidad para comprender cómo se construye un páncreas humano y servirá como base para el desarrollo de células pancreáticas a partir de células madre en medicina regenerativa”, concluye Ferrer.

Inês Cebola, Santiago A. Rodríguez-Seguí, Candy H-H. Cho, José Bessa, Meritxell Rovira, Mario Luengo, Mariya Chhatriwala, Andrew Berry, Joan Ponsa-Cobas, Miguel AngelMaestro, Rachel E. Jennings, Lorenzo Pasquali, IgnasiMorán, Natalia Castro, Neil A. Hanley, Jose Luis Gomez-Skarmeta, Ludovic Vallier y Jorge Ferrer. TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors. Nature Cell Biology. DOI: 10.1038/ncb3160

Identification of novel functions of nuclear envelope protein LEMD2 suggests possible links to rare diseases
02/05/2015

The nuclear envelope is an essential structure in cells of fungi, plants and animals. It regulates spatial organization of chromosomes inside the nucleus as well as communication between the nucleus and the surrounding cytoplasm. In addition, the nuclear envelope, composed by hundreds of different proteins and lipids, is essential for correct positioning of the nucleus within the cell. To understand the function of individual nuclear envelope proteins, the Askjaer group at the CABD has investigated the distribution of emerin and LEMD2. Both proteins are present in all animals, including the nematode Caenorhabditis elegans that is used as model in the Askjaer group. Emerin and LEMD2 were found in all tissues, but at surprisingly different concentrations, which suggest that the two proteins have specific functions in certain tissues. Moreover, during nuclear envelope assembly, which takes place at the end of each cell division, LEMD2 is recruited faster than emerin and participates in structural organization of the nucleus and anchoring of the nucleus within the cell. Although cells can divide and survive in the absence of LEMD2, they are hypersensitive to other perturbations of the nuclear envelope and timing of cell division is delayed.
In humans, mutations in nuclear envelope proteins, including emerin, cause rare diseases known as laminopaties. These diseases affect nuclear organization in multiple tissues and manifest as muscular dystrophies, neuropathies and premature aging. Research in model organisms is important to understand how the different mutations induce specific diseases and this work by the Askjaer group suggests that mutations in LEMD2 might contribute to tissue malfunction.

Inner nuclear membrane protein LEM-2 is required for proper nuclear separation and morphology. Adela Morales-Martínez, Agnieszka Dobrzynska, Peter Askjaer. Journal of Cell Science Advance Online Article February 4, 2015. doi: 10.1242/jcs.164202








Video Contest 2014



3rd price “Mouse CT scan"
Micro Computerized Tomography (µCT) scan of wild type mouse embryo at 14.5 days of gestation. Authors: Macarena López-Mayorga (1), Lydia Teboul (2) and Jaime J. Carvajal(1). [1.- CABD; 2.- MRC Harwell, UK]





2nd price "Intrusos en casa"
Time-lapse recording showing transplanted macrophages (in green) invading a Drosophila melanogaster embryo. Host embryo macrophages are marked in red. Author: Besaid Sanchéz. [CABD]





1st price "Bailar pegados"

Time-lapse recording showing random migration of macrophages (in green) in a stage 15 Drosophila melanogaster embryo. Author: Besaid Sanchéz. [CABD]






Keeping the balance between the sexes - a novel role of the nuclear envelope
02/12/2014

In species with several sexes, expression of genes on the sex-determining chromosome represents a particular challenge. In many species, including in humans, females contain two X chromosomes whereas males have a single copy. Because many essential genes are present on the X chromosome mechanisms are required to ensure that these genes are expressed equally in the two sexes. However, the precise regulation of this phenomenon, also known as dosage compensation, is poorly understood. In the nematode Caenorhabditis elegans, dosage compensation is achieved by twofold down-regulation of gene expression from both X chromosomes in hermaphrodites. The Askjaer lab at the CABD has participated in a study, which show that in males, the single X chromosome interacts with nuclear envelope proteins, while in hermaphrodites, a group of proteins called the dosage compensation complex impairs this interaction and alters X localization.

Rahul Sharma, Daniel Jost, Jop Kind, Georgina Gómez-Saldivar, Bas van Steensel, Peter Askjaer, Cédric Vaillant, and Peter Meister. Differential spatial and structural organization of the X chromosome underlies dosage compensation in C. elegans. Genes Dev. December 1, 2014 28: 2591-2596; doi:10.1101/gad.248864.114

Open House 2014



Composition and method for preserving and stabilizing apoptotic cells
01/09/2014

The research group of José Sánchez Alcázar has patented a composition and method for preserving and stabilizing apoptotic cells (PT 0049/2013).
Apoptosis is a controlled physiologically advantageous death process as apoptotic cells are removed by phagocytosis before cell content is released to the extracellular space. Therefore, apoptosis prevents the damage to surrounding cells and the induction of an inflammatory response. In the event of not being phagocytosed apoptotic cells undergo a process of secondary necrosis with the release of intracellular components which are cytotoxic and pro-inflammatory.
In our invention we present a method for the stabilization of apoptotic cells to ensure its temporal integrity and thus, preventing secondary necrosis.
Stabilization and preservation of apoptotic cells is of great interest in different applications:

• Quantification of apoptotic cells by diagnostic kits is a technique widely used to assess the cytotoxic effects of new compounds. This determination of apoptotic cells is often affected because in the process of handling many cells enter secondary necrosis and they are not accurately quantified. The use of the technology proposed in this invention will stabilize apoptotic cells and a more reliable quantification.
• Stabilization of apoptotic cells and delayed their entry into secondary necrosis is also important to avoid toxic and pro-inflammatory phenomena induced by cell death. Thus stabilization of apoptotic cells may be a protective mechanism to minimize the side effects in cancer therapy.
• Apoptotic cells are used for various forms of therapy, primarily with the aim of developing immunotolerance in the recipient individual. The stabilization of the apoptotic cells by the present invention ensures that the inoculated apoptotic cells retain their characteristic features until they are phagocytosed by macrophages.
• The stabilized apoptotic cells may also be used to transport substances such as therapeutic proteins in order to induce immunotolerance or for protein replacement therapy.
• There are forms of cell death (toxic, cold, etc.) whose characteristics impede the correct formation of the apoptotic microtubule network (AMN). As a result many side effects may emerge. The stabilization of apoptotic cells by the present invention can allow the development of new therapies to facilitate the correct formation and stabilization of the AMN and the induction of a more physiological and controlled type of cell death.

The research that originated the patent has been published in Cell Death and Disease, 2014, 5, e1369: Stabilization of apoptotic cells: generation of zombie cells.


Aging and nuclear organization: two (un-)related phenomena
31/03/2014

Understanding why and how organisms age has been one of the longest standing challenges to biology and medicine. As we age, many functions of our body are altered and we face an increasing risk of succumbing to diseases such as diabetes, cancers and Alzheimer. Reflecting the variety of changes in our physiology, several molecular mechanisms have been proposed to contribute to the normal aging process, including diminished capacity to repair damages in our DNA and dysfunction of the mitochondria that control cell metabolism. More recently, it was discovered that mutations in the nuclear lamina gene LMNA cause progeria accompanied by deterioration of morphology and organization of the nuclei of our cells. Progeroid syndromes are rare genetic disorders characterized by dramatically accelerated aging that typically affects children within 1-2 years after birth and is fatal at an early age. The link between aging and nuclear morphology has been reproduced in the nematode Caenorhabditis elegans. Further studies in this popular model system found that mutations that cause the animals to live longer also slowed down nuclear deterioration. In contrast, short-lived animals were observed to have accelerated nuclear deterioration. The observations in progeria patients and C. elegans suggested a functional relation between nuclear morphology and aging. However, recent studies at the Andalusian Centre for Developmental Biology (CABD) have demonstrated that animals can have an extended lifespan although the nuclei of their cells change morphology at the same rate as in animals with normal lifespan. The groups of Manuel J. Muñoz and Peter Askjaer analyzed different genetic and metabolic pathways and found that while longevity correlates with rate of nuclear deterioration in several cases, the correlation is not universal and is absent in animals with mutations in the gene encoding the C. elegans IGF/insulin receptor. These findings highlight the general nuclear deterioration observed during aging but also stress that changes in nuclear morphology do not necessarily alter lifespan.

Pérez-Jiménez MM, Rodríguez-Palero MJ, Ródenas E, Askjaer P, Muñoz MJ. (2014) Age-dependent changes of nuclear morphology are uncoupled from longevity in Caenorhabditis elegans IGF/insulin receptor daf-2 mutants. Biogerontology, doi: 10.1007/s10522-014-9497-0

Activity of neuronal and muscle genes requires the protein emerin to properly organize the genome
04/02/2014

All cells of our body – with a few exceptions – contain within their nucleus the same genetic information but cells in distinct organs differ in the way they utilize this information. For instance, intestinal cells express genes that produce enzymes required for efficient degradation and absorption of nutrients whereas neurons express genes that generate the signaling molecules that allow communication between neurons and from neurons to muscles. These are just two examples, but tissue-specific gene expression is a universal feature throughout the life of plants and animals. Different mechanisms have evolved to establish tissue-specific gene expression. One of these deals with where genes are positioned within the cell nucleus. Generally, genes that are positioned at the nuclear periphery are less expressed than genes away from the periphery. Moreover, binding of genes to proteins anchored at the nuclear periphery may influence their activity. Researchers at the CABD have now analyzed how two nuclear peripheral proteins, lamin and emerin, are involved in spatial organization of genes. Cristina González-Aguilera and co-workers used the popular model system Caenorhabditis elegans, but both proteins are highly conserved in the animal kingdom. In fact, these two proteins were chosen because when mutated in humans they can cause a range of diseases, including muscular dystrophies, neuropathies and premature aging. The CABD researchers, in collaboration with scientists from University of North Carolina at Chapel Hill and Center for Biomedical Research of La Rioja, found that lamin and emerin show a large overlap in the genes they interact with and that these interactions are mostly conserved throughout animal development. However, González-Aguilera and co-workers also discovered that genes expressed in neurons and muscles bind more frequently to emerin than to lamin. The researchers next analyzed animals lacking emerin, thus mimicking the situation in human Emery-Dreifuss muscular dystrophy patients. This revealed that absence of emerin causes both repositioning and deregulation of emerin and muscle genes. Most importantly, González-Aguilera and co-workers also found that communication from neurons to muscles is abnormal in animals lacking emerin, suggesting that anchoring of genes to emerin at the nuclear periphery of these cell types is critical for their proper function. If future experiments confirm these observations in human cell it may imply that development of Emery-Dreifuss muscular dystrophy involves altered nuclear architecture and gene expression, especially in muscles and neurons.

González-Aguilera et al.: Genome-wide analysis links emerin to neuromuscular junction activity in Caenorhabditis elegans. Genome Biology 2014 15:R21. doi:10.1186/gb-2014-15-2-r21

Descubren uno de los casos más extremos de evolución divergente descritos hasta la fecha.
06/01/2014

Durante la evolución animal las distintas partes del cuerpo se modifican, adaptándose para cumplir nuevas funciones. En los vertebrados, por ejemplo, esto ha hecho que las extremidades anteriores se hayan adaptado para formar alas, aletas o patas como adaptación a distintos modos de vida. Lo mismo ocurre en los invertebrados, donde observamos modificaciones en la forma de las patas adaptadas para la caza, como en la Mantis religiosa; o para el salto, como en langostas y saltamontes. En estos ejemplos los cambios evolutivos son relativamente pequeños y las variaciones morfológicas no impiden reconocer el órgano del que se originaron las nuevas estructuras. Sin embargo durante la evolución, a medida que las diferencias entre los órganos se acumulan, llega un momento en que es prácticamente imposible reconocer el origen de estos nuevos órganos. Estudiando los genes que controlan el desarrollo de la mosca de la fruta, científicos del CSIC trabajando en el Centro Andaluz de Biología del Desarrollo en la Universidad Pablo de Olavide de Sevilla describen en el último número de la prestigiosa revista Current Biology uno de los casos mas extremos de evolución conocidos hasta la fecha. Su trabajo muestra que los órganos respiratorios y las glándulas que controlan la metamorfosis de los insectos, a pesar de su extrema diferencia morfológica y funcional, se originaron a partir de estructuras idénticas. Los insectos carecen de un sistema circulatorio sanguíneo cerrado y el oxígeno llega a las células gracias a que las tráqueas forman un sistema de túbulos que se ramifican para llevar directamente el oxígeno desde el exterior. Las glándulas endocrinas que controlan la metamorfosis de la mosca no forman túbulos sino agregados de células que forman un anillo rodeando la apertura de la aorta, donde vierten sus hormonas. A pesar de su distinta forma y función, estos investigadores encuentran que, en ciertas condiciones mutantes, las glándulas pueden formar tráqueas y las tráqueas pueden formar glándulas, descubriendo el “parentesco” común de estos órganos que ha quedado escondido tras millones de años de evolución divergente. El origen común entre estos órganos también se evidencia en la utilización de genes similares para la construcción de ambos órganos y por el idéntico desarrollo embrionario temprano de las tráqueas y las glándulas. Ambas se forman a partir de grupos de células epidérmicas presentes en la misma posición de cada segmento. Estas células se internalizan en el cuerpo, y mientras que las células del tórax y el abdomen mantienen unidas al exterior dando lugar a los tubos traqueales; las células cefálicas pierden la organización epitelial, se independizan de la epidérmis externa y migran hacia la aorta donde se reagrupan formando las características glándulas en forma de anillo. Es especialmente interesante el descubrimiento de que la migración y la perdida de características epiteliales se deben a que las glándulas han reclutado un gen, snail, que en vertebrados está implicado en la migración invasiva de células tumorales. Este nuevo modelo de investigación es interesante no solo por sus implicaciones evolutivas, si no porque puede ayudar a entender porqué unas células epidérmicas, normalmente integradas en un tejido, pierden la cohesión y se convierten en migradoras; y porqué mientras que durante el desarrollo normal éstas células eventualmente dejan de migrar, en casos patológicos la capacidad migratoria se mantiene y las células invaden múltiples órganos.

Sánchez-Higueras, C., Sotillos, S. and Castelli-Gair Hombría J. (2014). Common origin of insect trachea and endocrine organs from a segmentally repeated precursor. Current Biology. 24, 76-81

1st CABD Workshop: Applied Technologies for Aquatic Vertebrates
01/04/2013

Venue: Aquatic Vertebrate Platform
Centro Andaluz de Biología del Desarrollo-CSIC-UPO
Registration Opens Date: Monday, April 1, 2013
Registration Deadline: Monday, April 22, 2013
Acceptance Notification Date: Wednesday, April 24, 2013
Participation: Limited number of participants.
Date: 27 May to 6 June

Contact: Ana Fernández Miñán
e-mail: amfermin(at)upo(dot)es
Tel: +34 954 977445
web: Aquatic Vertebrates Platform 

More information here:
-Flyer CABD Workshop AVP
-Workshop AVP Info
-Workshop AVP Preliminary Programme
-Workshop AVP Registration

Die, but die responsibly
9/03/2013

Cell death happens all the time: during normal development to shape brains or fingers, or to remove the surplus of lymphocytes after a won battle, and often also during disease. Therefore cell death cannot be used too liberally. If a dying cell were just simply to die and release its content, many active enzymes could then chemically attack the healthy neighbors. It might also call for immune cells to mount an inflammatory response against the normally confined content of the expiring cell causing unnecessary havoc. However, physiological cell death occurs in a regulated, step-wise manner called apoptosis. During this process, the designated apoptotic cell triggers a cascade of proteolytic events that chops into pieces its components. These “death proteases” are called caspases, and are extremely voracious. So, then, how come that they do not devour the many proteins that help holding together the plasma membrane, causing the spilling out of the cell’s content –including the caspases themselves? The Sánchez-Alcázar lab, at the CABD, has discovered that in order to prevent caspase access to the membrane, the dying cells build a protecting shield just underneath the membrane made of microtubules –a sort of impermeable scaffolding. So, while the cell is swiftly disposing of its proteins and DNA, the membrane remains functional. This might help the removal of the apoptotic cell by macrophages and avoid what experts call necrosis –the uncontrolled and potentially pathogenic cell death. For more information, please check: Apoptotic microtubules delimit an active caspase free area in the cellular cortex during the execution phase of apoptosis. Cell Death and Disease (2013) 4, e527- (FC, CABD News).

A new patent describes a method for assessing drugs as new therapeutics for MELAS.[“Method for screening / assessment of the effectiveness of drugs for treatment of MELAS syndrome and mitochondrial diseases. PT 0036/2012”]
9/03/2013

MELAS (mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes) syndrome is a mitochondrial disease most usually caused by point mutations in mitochondrial tRNA (MTT) genes. In this invention, the Sánchez-Alcázar lab proposes to consecutively use three cellular MELAS models (yeasts, fibroblast and cybrids) for the screening and evaluation of the effectiveness of new drug treatments for the disease. A pilot study of this methodology has been recently published: Screening of effective pharmacological treatments for MELAS syndrome using yeasts, fibroblasts and cybrids models of the disease. 
British Journal of Pharmacology, 2012, 167(6):1311-28.

Making sense of a chemical map.
11/12/2012

Cells in a developing tissue are like small computers, capable of processing the information coming from local neighbors and distant hormone-producing organs. One specially important is positional information: it allows cells to adopt particular fates in the right place within an organ. Positional information is conveyed by chemical signals, often called morphogens. These chemicals are produced by specialized groups of cells which, like beacons, are used as positional references. Hedgehog (Hh) molecules act as such signals. Hh molecules, which are conserved in evolution, play innumerous roles during development, from the generation of neuronal diversity across the neural tube, through the identity of fingers in a hand to the patterning of a fly retina. And often tumors show aberrant Hh signaling. However, it still poorly understood how the chemical gradient of Hh molecules is processed by cells to acquire different fates according to their position within this flow of Hh.
By using a simple and genetically tractable organ system, the simple eyes (or ocelli) of the fruitfly, Aguilar-Hidalgo, Domínguez-Cejudo and co-workers obtain a first answer to this problem: the architecture of the gene network of the cells is such that a continuous Hh gradient is translated into a binary cell fate choice: either to become photoreceptor, or ectodermal cell. This choice is made so that not only the two fates are realized, but the right number of each cell type is produced. Mathematical modeling reveals potential properties of such a system. First, it is resilient to noise (that is, biochemical fluctuations should be buffered, so that even if they existed, the final ocellar structure would not be perturbed). Second, after a massive parameter space exploration, the modeling suggests that continuous variations in reactions constants (as expected by slow, cumulative mutations during evolution) can give rise to discontinuous variations in morphologies –a bit like a jumping morphological evolution. In addition, the system described by the authors shows some tantalizing parallels with the Hh-controlled system that generates motorneuron diversity in the spinal cord of vertebrates. Therefore, the paper opens a number of questions that relate to the function of Hh morphogens in specifying cell types and the role played by the responding cellular networks in the stability and evolution of the organs these morphogens control.
More information can be found in: A Hh-driven gene network controls specification, pattern and size of the Drosophila simple eyes. Aguilar-Hidalgo D, Domínguez-Cejudo MA, Amore G, Brockmann A, Lemos MC, Córdoba A, Casares F. Development. 2013 Jan;140(1):82-92. doi: 10.1242/dev.082172. Epub 2012 Nov 15.

Gimme a hand
11/12/2012

During the Devonian, and for a period that lasted some 10 million years, some fish-like creatures were lurking in murky, shallow waters. Some would make it out of the water, colonizing the land, back then a real land of (ecological) opportunities. These land-colonizers were our ancestors. Their evolutionary journey entailed numerous morphological and physiological adaptations, including using lungs for breathing or modifying their skin to prevent dessication. But one of the key innovations was the development of stronger limbs capable of sustaining their weight outside the water, allowing them to move around. This required the elaboration of the distal fin of these ancestral animals, an elaboration that, as eons passed, generated the hands and feet of extant tetrapods, with their great variety of forms and adaptations, including the human hand –perhaps the most sophisticated mechanical tool produced by evolution. How did this distal elaboration begin? Developmental Biology went in Paleontology´s aid. First, the hand in extant tetrapods requires a burst in expression of a set of Hox genes, including Hoxd13, in the tip of the developing limb bud. In the absence of this transcription factor, the hand/foot region (the so-called autopod) is missing. And this burst is tetrapod specific. Second, this tetrapod-specific Hoxd13 burst required tetrapod-specific DNA control regions (or CREs). Therefore, the hypothesis was that the acquisition of novel CREs might have increased hoxd13 expression in the tip of the fin bud of one of those ancestors, leading to the generation of new bone material. These new bones would have been useful to its bearer, leading to the further elaboration of the distal fin into a proto-hand and beyond through further variation and selection. But what about the functional proof? As going back to the Devonian is out of the question, Renata Freitas and co-workers used an evolutionary reasoning: if a character is present in two animal groups, it must have been present in the last common ancestor of both groups. In the fish-to-limb issue, this translates as: if an extant fish were able to generate an autopod like structure under certain condition, like a tetrapod, this capacity must have existed already in the last common ancestor of fish and tetrapods –our shallow water dweller ancestor. So Renata set to test this in the “handy “ zebrafish. First, she mimicked a burst of hoxd13 expression in the developing tip of a zebrafish fin. The resulting fins showed higher growth and the formation of new cartilage (that preceded bone) with distal (i.e. tip) identity, as shown by a number of molecular markers, very much like a developing mouse limb bud would do. This transformation ran parallel to the thinning of the ectodermal component of the fin (that gives rise to the radials in fish fins), recapitulating what paleontologists have observed in the fossil record. Second, one tetrapod-specific CRE, with known tip activity in the mouse limb, was introduced in the fish. This CRE controls the expression of the fluorescent protein GFP and the transgenic fish showed a green glow at the tip of their fins, again very much like this mouse CRE does in its normal context –the mouse limb. Therefore, even after so many years of evolution, an extant fish genome “knows” how to activate a tetrapod specific CRE in the right place and to orchestrate a response downstream of Hoxd13 to generate the “right” type of tissue. Quite something for a humble fish. But the key thing is that evolutionary reasoning: if today’s fishes can do it, our last common ancestor could do it too. So here you have the functional proof to the hypothesis, coarsely rerunning a 10 million years tape in a 2 day experiment!
For further information: Hoxd13 Contribution to the Evolution of Vertebrate Appendages. Renata Freitas, Carlos Gómez-Marín, Jonathan Mark Wilson, Fernando Casares, José Luis Gómez-Skarmeta. Developmental Cell. 11 December, 2012 Volume 23, Issue 6


Mechanisms controlling the cells’ grip to their substratum explains the origami of eye morphogenesis.
08/10/2012

The eye balls derive from the lateral outpocketting of the embryonic anterior neural tube. However, this sac must fold to form a cup before becoming a real eye. Its inner surface will develop into the light-sensing retina and will hold inside the forming lens, very much like a baseball glove catching a ball. This act of epithelial origami is essential, as the shape of the eye determines its optical properties–and its function thereof. The gene ojoplano (Opo, “flateye” in its Spanish translation) was known to be required for the retinal folding. The work published now by the Martínez-Morales lab (CABD, Sevilla) throws light into the mechanisms controlled by Opo. Tissue movement often relies on the ability of the tissue to exert forces onto the extracellular matrix. Its grip is mediated by integrins, which link cells to their substrate matrix. Opo regulates the dynamics of attachment/detachment to the matrix by regulating the availability of integrins on the cells surface. The paper reveals that Opo regulates the activity Numb and Numbl which results into the slowing down of integrin removal from the cells’ basal surface, which takes place within specialized vesicles coated with the protein clathrin. This preferential action on the basal, versus apical cell sides is critical, as it generates asymmetric tensions within the epithelium which, ultimately, leads to its shaping into a cup, prefiguring the shape of the final, functional eye. The experiments were carried out in the Medaka fish (which, very conveniently, has enormous, bulging embryonic eyes) and in collaboration with groups at the CABIMER (Sevilla) and the University of Heidelberg. The paper is now published (on-line version) in Developmental Cell (Numb/Numbl-Opo Antagonism Controls Retinal Epithelium Morphogenesis by Regulating Integrin Endocytosis, by Ozren Bogdanović, Mariana Delfino-Machín, María Nicolás-Pérez, María P. Gavilán, Inês Gago-Rodrigues, Ana Fernández-Miñán, Concepción Lillo, Rosa M. Ríos, Joachim Wittbrodt and Juan R. Martínez-Morales).

Link between chromatin dance and gene expression control unveiled.
14/09/2012

The DNA in the genome is wrapped in spirals around globules of proteins called histones. This spiraling allows the packing of a meter-long genome to fit within the tiny nucleus of each cell. Its degree can vary, though: regions with lose packing are “open for business” –that is, these DNA segments can be copied and thus genes can be expressed. However, other regions are very compact and remain silent. Since cell function requires a perfectly regulated gene expression control, any alteration in DNA packing can lead to abnormal gene expression and thus to disease. Interestingly, the active and inactive chromatin bits are segregated to different regions within the nucleus: active chromatin goes to the center, while the inactive or silent chromatin locates at the periphery, attached to the nucleus’ envelope. Compaction of the chromatin into silent DNA requires the chemical modification of the H3 histone on a key aminoacid residue into the H3K9me3 form. The Gasser (Friedrich Miescher Institute for Biomedical Research, Switzerland) and Askjaer (CABD, Spain) teams have identified two enzymes, MET-2 and SET-25, acting in successive steps, as the ones responsible for the modification of histone H3 at the nuclear envelop in the worm C. elegans. Thereby, these enzymes muzzle some regions of the genome and lock them in the nuclear envelop. These two processes are reversible, allowing for dynamic gene regulation. This study appears in the 31 August 2012 issue of the journal Cell. Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery. Towbin BD, González-Aguilera C, Sack R, Gaidatzis D, Kalck V, Meister P, Askjaer P, Gasser SM. (2012). Cell, 150, 934-47.

New CABD director.


From May 2011 Dr Eduardo Santero Santurino is our new director. He has become the fourth CABD director in substitution of Dr Acaimo González-Reyes that successfully lead the centre since 2007.