Proteogenomiikan hyödyntäminen translatiivisessa syöpätutkimuksessa

Cancer continues to be a major clinical and societal challenge. Globally, the cancer burden rises every year with a new record of 18.1 million new cases and 9.6 million cancer deaths, as reported by the World Health Organization. Despite the increased financial efforts of western countries to cure this disease, it is expected that in the year 2040, over one-third of the population will be diagnosed with cancer. The gap in translating basic research into clinical benefit requires cross-disciplinary approaches to harness large data from the complex molecular systems and cellular organization within the tumor. The main obstacles in current cancer care are late detection and therapy resistance. While high-throughput and single-cell methodologies have become an advisable tool to analyze molecular profiles, their use for clinical decision-making is still missing. This thesis aims to propose efficient methodologies to connect molecular and cellular profiling research to cancer therapy outcomes. In the first and second publications, we made available software to rapidly analyze large mass cytometry data with high resolution and interaction-assisted interpretation steps for the analysis. These methods allow the rapid profiling of tumor cell populations and their association with therapy response. As part of the third project, we developed new image analysis methods to identify therapy response predictors from highly multiplexed images. We found that spatial organization within the tumor microenvironment was highly associated with DNA damage genome scarring. In the fourth study, we designed a new method to identify epigenetically reversible drug resistance mechanisms in tumor cells. The application of novel methodologies contributed to a better understanding of the roles of genomic and proteomic features in the tumor-immune microenvironment in response to modern anti-cancer therapies.Syöpä on edelleen merkittävä kliininen ja yhteiskunnallinen haaste. Maailmanlaajuisesti syöpätapausten määrä nousee vuosittain, uuden ennätyksen ollessa Maailman terveysjärjestö WHO:n mukaan 18,1 miljoonaa uutta tapausta ja 9,6 miljoonaa syöpäkuolemaa. Huolimatta länsimaiden lisääntyneistä taloudellisista ponnisteluista tämän taudin parantamiseksi, on odotettavissa, että vuonna 2040 yli kolmanneksella väestöstä tullaan diagnosoimaan syöpä. Aukko perustutkimuksen muuntamisessa kliiniseksi hyödyksi vaatii monialaisia ​​lähestymistapoja, jotta voidaan hyödyntää suuria määriä dataa kasvaimen sisäisistä monimutkaisista molekyylijärjestelmistä ja solurakenteesta. Suurimmat esteet nykyisessä syöpähoidossa ovat myöhäinen havaitseminen ja hoitoresistenssi. Vaikka suuritehoisesta tutkimuksesta, eli automatisoinnin avulla tehostetusta mittauksesta, ja yksittäisen solutason tutkimusmenetelmistä on tullut suositeltu työkalu molekyyliprofiilien analysointiin, niiden käyttö hoitopäätösten teossa puuttuu yhä. Tämän tutkielman tarkoituksena on esittää tehokkaita menetelmiä molekyylien ja solujen profilointitutkimuksen yhdistämiseksi syöpähoitojen tuloksiin. Ensimmäisessä ja toisessa julkaisussa kehitimme ohjelmiston, jolla voidaan analysoida nopeasti suuren kokoluokan massasytometriadataa korkealla resoluutiolla ja hyödyntää interaktiivisia tulkintavaiheita analyysissä. Nämä menetelmät mahdollistavat kasvainsolukantojen nopean profiloinnin ja niiden yhdistämisen hoitovasteeseen. Kolmannen projektin osana kehitimme uusia kuva-analyysimenetelmiä hoitovastetta ennustavien markkereiden tunnistamiseksi erittäin monikanavaisista kuvista. Havaitsimme, että solujen järjestäytyminen kasvaimen mikroympäristössä oli voimakkaasti yhteydessä DNA-vaurion aiheuttamaan genomin arpeutumiseen. Neljännessä tutkimuksessa suunnittelimme uuden menetelmän epigeneettisesti kumottavien lääkeresistenssimekanismien tunnistamiseksi kasvainsoluissa. Uusien tutkimusmenetelmien soveltaminen johti parempaan ymmärrykseen genomin ja proteomin ominaisuuksien roolista kasvaimen immuunimikroympäristössä ja niiden merkityksestä nykyaikaisten syöpähoitojen vasteeseen

CASO CLÍNICO DE UN PACIENTE CON DÉFICIT SOMATOSENSORIAL TRAS SUFRIR UN ICTUS ISQUÉMICO IZQUIERDO.

"INTRODUCCIÓN: LAS ENFERMEDADES CARDIOVASCULARES CONSTITUYEN UNO DE LOS PRINCIPALES PROBLEMAS DE SALUD EN LOS PAÍSES DESARROLLADOS. LA ALTERACIÓN SOMATOSENSORIAL SUCEDE EN EL 50-80% DE LOS SUPERVIVIENTES DEL ICTUS. HASTA EL 80% DE LAS PERSONAS QUE TIENEN UN ACCIDENTE CEREBROVASCULAR SUFRE PÉRDIDA SENSORIAL EN EL BRAZO AFECTADO, LO QUE SUPONE MAYOR RIESGO DE LESIÓN E INFLUYE EN EL USO FUNCIONAL Y NIVEL DE INDEPENDENCIA. OBJETIVOS: DESARROLLAR Y EVALUAR UNA INTERVENCIÓN TERAPÉUTICA FISIOTERÁPICA BASADA EN LA EVIDENCIA EN UN CASO CLÍNICO DE ICTUS ISQUÉMICO IZQUIERDO CON GRAN AFECTACIÓN SOMATOSENSORIAL, ADEMÁS DE MEJORAR LA FUNCIONALIDAD DEL HEMICUERPO AFECTO PARA RECUPERAR LA AUTONOMÍA DEL PACIENTE. MATERIAL Y MÉTODOS: EL ESTUDIO CONSISTE EN LA EVALUACIÓN E INTERVENCIÓN DE UN PACIENTE DEL HOSPITAL GENERAL UNIVERSITARIO DE ELCHE, QUE SUFRIÓ UN ICTUS ISQUÉMICO IZQUIERDO. TRAS UNA PRIMERA VALORACIÓN FISIOTERÁPICA IDENTIFICANDO LOS DÉFICITS Y NECESIDADES DEL PACIENTE, OBTUVIMOS EL DIAGNÓSTICO FISIOTERÁPICO Y LOS OBJETIVOS CORRESPONDIENTES. UNA VEZ ESTABLECIDOS LOS OBJETIVOS, IDENTIFICAMOS Y DISEÑAMOS EL TRATAMIENTO MANUAL FISIOTERÁPICO CON EL FIN DE APLICARLO. UNA VEZ APLICADO EL TRATAMIENTO SE REALIZÓ UNA SEGUNDA VALORACIÓN CON LA QUE ANALIZAMOS EL PROGRESO Y EVOLUCIÓN DE NUESTRO PACIENTE. RESULTADOS: ENCONTRAMOS UNA MEJORÍA SIGNIFICATIVA EN LA SENSIBILIDAD Y LAS HABILIDADES MOTORAS QUE INFLUYEN DE FORMA POSITIVA EN EL DESEMPEÑO DE LAS AVD. CONCLUSIONES: LA MAYORÍA DE LAS TÉCNICAS DESCRITAS EN EL TRATAMIENTO DEL DÉFICIT SOMATOSENSORIAL TRAS EL ICTUS SE BASAN FUNDAMENTALMENTE EN LA EVIDENCIA CLÍNICA, SIENDO LA EVIDENCIA CIENTÍFICA ESCASA. SE NECESITARÍA PROFUNDIZAR EN LA INVESTIGACIÓN EN ESTE CAMPO DE LA FISIOTERAPIA.

Más allá de la venta: el consumidor y el sector funerario en previsión

El trabajo que se muestra a continuación es el fruto de una investigación centrada en descubrir qué mecanismos configuran la percepción del consumidor sobre el sector funerario en previsión. Se ha definido el sector a través de 3 elementos a estudiar: seguro de decesos, testamento y documento de instrucciones previas. Este es un viaje que parte de la herencia cultural, pasando por sus conceptos legales y características de marketing para ayudar a explicar lo que supone este sector actualmente. Para comprender a la sociedad española, se adentra en lo que piensa el consumidor gracias al uso de técnicas cuantitativas y cualitativas que revelan en que orden de respuesta les influyen las características personales. Los resultados son claros: la muerte aún es un tema tabú, más si cabe entre jóvenes, lo que hace que este sector sea ignorado completamente.The essay shown below is the result of research focused on discovering what mechanisms shape the consumer's perception of the funeral industry in advance. The industry has been defined through 3 elements for study: death insurance, will and advance health care directives. This is a journey that starts with the cultural heritage, going through its legal concepts and marketing characteristics to help explain what this industry currently supposes. To understand Spanish society, it delves into what the consumer thinks through the use of quantitative and qualitative techniques that reveal in which response order personal characteristics influence it. The results are clear: death is still a taboo subject, even more so among young people, which means that this sector is completely ignored.Departamento de Organización de Empresas y Comercialización e Investigación de MercadosGrado en Marketing e Investigación de Mercado

La materialización de las desigualdades sociales a través del mundo funerario: una aproximación a las sociedades costeras del Mesolítico tardío europeo

35 p.: il.-- Bibliogr.: p. 27-30Este trabajo pretende, mediante una aproximación teórica basada en una revisión bibliográfica, definir, analizar y ejemplarizar las desigualdades en la organización social de los grupos de cazadores-recolectores costeros del Mesolítico tardío en la Europa atlántica, todo ello a través de la evidencia arqueológica que nos ofrece el mundo funerario. Para ello, hemos definido las principales formas de estratificación social (horizontal y vertical) en sociedades cazadoras-recolectoras desde un punto de vista etnográfico y, posteriormente, contextualizado estas hipótesis en el Mesolítico tardío de la costa Atlántica europea. De manera análoga, la evidencia arqueológica relativa al mundo funerario de los yacimientos franceses de Téviec y Hoëdic (ambos en Quiberon) y el conjunto arqueológico de Vedbaek (Dinamarca), todos ellos situados en la costa, con necrópolis y asociados al Mesolítico reciente y tardío, han proporcionado los datos necesarios para analizar la organización social de los grupos que habitaron dichos lugares. Restos animales, útiles, adornos, elementos que indican un uso ritual y análisis isotópicos relativos a la dieta son los elementos estudiados para obtener ejemplos tangibles de diferencias de trato funerario o de modo de vida entre individuos. Los datos, contrastados con la teoría etnográfica y comparados con yacimientos similares, muestran una variabilidad en las prácticas funerarias. Esta variabilidad, además de circunstancial y fruto de preferencias locales, puede responder a patrones ligeramente asociados a una segmentación social principalmente horizontal, en la que el estatus de ciertos individuos es adquirido y variable, sin claros indicios de heredabilidad. No obstante, aún se necesitan análisis más amplios (en lo referido a métodos tanto como a estudio de más yacimientos) para poder crear una imagen más detallada de la realidad de estos grupos de cazadores-recolectores del Mesolítico tardío

The Ksar Ghilane 002 shergottite-The 100th registered Martian meteorite fragment

We report on the discovery of a new shergottite from Tunisia, Ksar Ghilane (KG) 002. This single stone, weighing 538 g, is a coarse-grained basaltic shergottite, mainly composed of maskelynitized plagioclase (approximately 52 vol%) and pyroxene (approximately 37 vol%). It also contains Fe-rich olivine (approximately 4.5 vol%), large Ca-phosphates, including both merrillites and Cl-apatites (approximately 3.4 vol%), minor amounts of silica or SiO_2-normative K-rich glass, pyrrhotite, Ti-magnetite, ilmenite, and accessory baddeleyite. The largest crystals of pyroxene and plagioclase reach sizes of approximately 4 to 5 mm. Pyroxenes (Fs_(26–96)En_(5–50)Wo_(2–41)). They typically range from cores of about Fs_(29)En_(41)Wo_(30) to rims of about Fs_(68)En_(14)Wo_(17). Maskelynite is Ab_(41–49)An_(39–58)Or_(1–7) in composition, but some can be as anorthitic as An_(93). Olivine (Fa_(91–96)) occurs mainly within symplectitic intergrowths, in paragenesis with ilmenite, or at neighboring areas of symplectites. KG 002 is heavily shocked (S5) as indicated by mosaic extinction of pyroxenes, maskelynitized plagioclase, the occurrence of localized shock melt glass pockets, and low radiogenic He concentration. Oxygen isotopes confirm that it is a normal member of the SNC suite. KG 002 is slightly depleted in LREE and shows a positive Eu anomaly, providing evidence for complex magma genesis and mantle processes on Mars. Noble gases with a composition thought to be characteristic for Martian interior is a dominant component. Measurements of ^(10)Be, ^(26)Al, and ^(53)Mn and comparison with Monte Carlo calculations of production rates indicate that KG 002 has been exposed to cosmic rays most likely as a single meteoroid body of 35–65 cm radius. KG 002 strongly resembles Los Angeles and NWA 2800 basaltic shergottites in element composition, petrography, and mineral chemistry, suggesting a possible launch-pairing. The similar CRE ages of KG 002 and Los Angeles may suggest an ejection event at approximately 3.0 Ma

SREBP-1a activation by HBx and the effect on hepatitis B virus enhancer II/core promoter

Hepatitis B virus (HBV) X protein (HBx) plays an important role in HBV pathogenesis by regulating gene expression. Sterol regulatory element binding protein-1a (SREBP-1a) is a key transcriptional factor for modulating fatty acid and cholesterol synthesis. Here we demonstrated that HBx increased mature SREBP-1a protein level in the nucleus and its activity as a transcription factor. We further showed that the up-regulation of SREBP-1a by HBx occurred at the transcriptional level after ectopic expression and in the context of HBV replication. Deletional analysis using SREBP-1a promoter revealed that the sequence from -436 to -398 in the promoter was required for its activation by HBx. This promoter region possesses the binding sequences for two basic leucine zipper (b-ZIP) transcription factors, namely C/EBP and E4BP4. Mutagenesis of the binding sequences on the SREBP-1a promoter and ectopic expression experiments demonstrated that C/EBPα enhanced SREBP-1a activation by HBx, while E4BP4 had an inhibitory effect. C/EBPα was able to significantly reverse the inhibitory activity of E4BP4 on SREBP-1a promoter. These results demonstrated that HBx activates SREBP-1a activity at the transcription level through a complex mechanism involving two bZIP transcription factors C/EBP and E4BP4 with C/EBP being the dominant positive factor. Finally, we showed that knocking down SREBP-1 abolishes HBV enhancer II/core promoter activation by HBx.Fil: Qiao, Ling. University Of Saskatchewan; CanadáFil: Wu, Qi. University Of Saskatchewan; CanadáFil: Lu, Xinya. University Of Saskatchewan; CanadáFil: Zhou, Yan. University Of Saskatchewan; CanadáFil: Fernández Alvarez, Ana Julia. Consejo Superior de Investigaciones Cientificas; España. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Ye, Lihong. Nankai University; ChinaFil: Zhang, Xiaodong. Nankai University; ChinaFil: Han, Jihong. Nankai University; ChinaFil: Casado, Marta. Consejo Superior de Investigaciones Cientificas; EspañaFil: Liu, Quiang. University Of Saskatchewan; Canad

Drug screening approach combines epigenetic sensitization with immunochemotherapy in cancer

Background The epigenome plays a key role in cancer heterogeneity and drug resistance. Hence, a number of epigenetic inhibitors have been developed and tested in cancers. The major focus of most studies so far has been on the cytotoxic effect of these compounds, and only few have investigated the ability to revert the resistant phenotype in cancer cells. Hence, there is a need for a systematic methodology to unravel the mechanisms behind epigenetic sensitization. Results We have developed a high-throughput protocol to screen non-simultaneous drug combinations, and used it to investigate the reprogramming potential of epigenetic inhibitors. We demonstrated the effectiveness of our protocol by screening 60 epigenetic compounds on diffuse large B-cell lymphoma (DLBCL) cells. We identified several histone deacetylase (HDAC) and histone methyltransferase (HMT) inhibitors that acted synergistically with doxorubicin and rituximab. These two classes of epigenetic inhibitors achieved sensitization by disrupting DNA repair, cell cycle, and apoptotic signaling. The data used to perform these analyses are easily browsable through our Results Explorer. Additionally, we showed that these inhibitors achieve sensitization at lower doses than those required to induce cytotoxicity. Conclusions Our drug screening approach provides a systematic framework to test non-simultaneous drug combinations. This methodology identified HDAC and HMT inhibitors as successful sensitizing compounds in treatment-resistant DLBCL. Further investigation into the mechanisms behind successful epigenetic sensitization highlighted DNA repair, cell cycle, and apoptosis as the most dysregulated pathways. Altogether, our method adds supporting evidence in the use of epigenetic inhibitors as sensitizing agents in clinical settings.Peer reviewe

High-throughput mapping of cell wall glycans to unveil cell wall disassembly, a key process determining strawberry fruit softening

The short shelf life of strawberry fruit is a major limitation that produces important economic losses related to postharvest spoiling. Fruit texture of fleshy fruits is a complex trait but mainly rely on mechanical properties of parenchyma cell walls. Several studies support the relevance of cell wall modifying enzymes on cell wall deconstruction, decreasing cell wall strength and cell to cell adhesion, and ultimately producing the softening of the fruit at macroscopic level. Previous studies on our group showed that transgenic silencing of ripening-specific genes encoding some of these enzymes reduced softening and increased postharvest shelf life in strawberry (Fragaria × ananassa, cv. ‘Chandler’) fruits. In this research, to further investigate the cell wall remodelling process associated to strawberry softening a high-throughput analysis of cell wall composition based on monoclonal antibodies against different polysaccharide epitopes has been performed. To this purpose, cell walls were isolated from non-transgenic fruits at different developmental stages as well as from ripe fruits of selected transgenic lines with genes involved in metabolism of pectins (pectate lyase, polygalacturonase, β-galactosidase, pectin acetil esterase), hemicellulose/cellulose (endo-β-glucanase) or lignin (cinnamyl alcohol dehydrogenase) down-regulated. These transgenic lines showed a large variability in fruit firmness at ripening. Cell walls were fractionated and subjected to a carbohydrate microarray. The results obtained unveiled a common pattern of cell wall composition on those transgenic lines with firmer phenotypes, specially defined by the higher content of pectins on those cell wall fractions more imbricated in the matrix, which can be interpreted as a less degraded cell wall structure.This research was supported by FEDER EU Funds and the Ministerio de Economía y Competitividad of Spain (grant reference AGL2017-86531-C2-1-R). Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

qSNE: quadratic rate t-SNE optimizer with automatic parameter tuning for large datasets

Peer reviewe

Agile workflow for interactive analysis of mass cytometry data

Motivation: Single-cell proteomics technologies, such as mass cytometry, have enabled characterization of cell-tocell variation and cell populations at a single-cell resolution. These large amounts of data, require dedicated, interactive tools for translating the data into knowledge. Results: We present a comprehensive, interactive method called Cyto to streamline analysis of large-scale cytometry data. Cyto is a workflow-based open-source solution that automates the use of state-of-the-art single-cell analysis methods with interactive visualization. We show the utility of Cyto by applying it to mass cytometry data from peripheral blood and high-grade serous ovarian cancer (HGSOC) samples. Our results show that Cyto is able to reliably capture the immune cell sub-populations from peripheral blood and cellular compositions of unique immune- and cancer cell subpopulations in HGSOC tumor and ascites samples.Peer reviewe