5,171 research outputs found

    Therapeutic and prognostic strategies in neuroblastoma : exploring nuclear hormone receptors, MYC targets, and DIAPH3

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    Neuroblastoma (NB) is a pediatric cancer derived from the cells of neural crest origin that form the sympathoadrenal system. Typically, the tumor cells migrate along the spinal cord and spread to the chest, neck, and/or abdomen. Different clinical behaviors are observed in this disease: some tumors spontaneously regress without treatment, while others are highly aggressive and resistant to current therapies. Approximately 40% of high-risk NB patients have MYCN amplification while 10% have MYC (i.e. encoding c-MYC) overexpression. These patients have undifferentiated tumors with a poor prognosis. Our group previously found that the expression and activation of nuclear hormone receptors (NHRs) estrogen receptor alpha (ERα) by 17-β-estradiol (E2), and the glucocorticoid receptor (GR) by dexamethasone (DEX), could trigger differentiation by disrupting the regulation of the miR-17 ~ 92 microRNA cluster by MYCN. In paper I, we sought to investigate whether the simultaneous activation of both ERα and GR has a more beneficial effect compared to the activation of either ERα or GR alone. We examined cell survival, alterations in cell shape as indicated by neurite extension, variations in metabolic pathways, accumulation of lipid droplets, and performed xenograft experiments. Our findings revealed that the simultaneous activation of GR and ERα, compared to their single activation, led to reduced viability and a more robust differentiation. This dual activation also caused changes in glycolysis and oxidative phosphorylation, increased lipid droplet accumulation, and decreased aggressiveness in mouse models. The triple activation with an additional activation of the retinoic acid receptor using all trans-retinoic acid (ATRA), amplified the differentiation phenotype. Bulk-sequencing analysis showed that patients with high levels of NHRs are related to favorable survival and clinical outcome. In summary, our data suggest that combination activation of these NHRs could be a potential differentiation induction treatment. Paper II investigates target genes of c-MYC and MYCN to explore if it is possible to obtain a better prognosis prediction using the expression of this group of genes, instead of the expression of MYC and/or MYCN alone. In addition, we analyzed if there are different prediction power capabilities between c-MYC and MYCN target genes, and their different role during sympathoadrenal development. We screened lists of target genes by using comprehensive approaches, including differential expression analysis between clinical risk groups, INSS stages, MYCN amplification status, progression status; Univariate Cox regression analysis to select the target genes related to prognosis prediction power, and protein interaction network analysis to select genes that share a meaningful biology function. Following the training and validation of (LASSO) regression prediction models in three different patient cohorts (SEQC, Kocak, and Versteeg), we found that a risk score computed on c-MYC/MYCN target genes with prognostic value, could effectively classify patients in groups with different survival probabilities. The high-risk group of patients exhibited unfavorable clinical outcomes and low survival rates. Further, single cell RNA sequencing analysis revealed that c-MYC and MYCN targets have different expression patterns during sympathoadrenal development. Notably, genes linked to adverse outcomes were predominantly expressed in sympathoblasts in comparison to chromaffin cells. In summary, our research provides new insights into the importance of c-MYC/MYCN target genes during sympathoadrenal development and their value in predicting patient outcome. In paper III we studied the function of one member of the formin protein family involved in cytoskeleton modulation: Diaphanous Related Formin 3 (DIAPH3). We found that high DIAPH3 expression in NB tumors are associated with MYCN amplification, higher stage, risk, progression and negative clinical outcome. Elevated DIAPH3 expression was also found in specific cells during mouse sympathoadrenal development and in progenitor cells of the post- natal human adrenal gland. Furthermore, the knockdown of DIAPH3 resulted in a slight decrease in cell growth and cell cycle arrest. Our study suggests that DIAPH3 could be a promising target for new therapeutic strategies

    Converging organoids and extracellular matrix::New insights into liver cancer biology

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    Converging organoids and extracellular matrix::New insights into liver cancer biology

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    Primary liver cancer, consisting primarily of hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), is a heterogeneous malignancy with a dismal prognosis, resulting in the third leading cause of cancer mortality worldwide [1, 2]. It is characterized by unique histological features, late-stage diagnosis, a highly variable mutational landscape, and high levels of heterogeneity in biology and etiology [3-5]. Treatment options are limited, with surgical intervention the main curative option, although not available for the majority of patients which are diagnosed in an advanced stage. Major contributing factors to the complexity and limited treatment options are the interactions between primary tumor cells, non-neoplastic stromal and immune cells, and the extracellular matrix (ECM). ECM dysregulation plays a prominent role in multiple facets of liver cancer, including initiation and progression [6, 7]. HCC often develops in already damaged environments containing large areas of inflammation and fibrosis, while CCA is commonly characterized by significant desmoplasia, extensive formation of connective tissue surrounding the tumor [8, 9]. Thus, to gain a better understanding of liver cancer biology, sophisticated in vitro tumor models need to incorporate comprehensively the various aspects that together dictate liver cancer progression. Therefore, the aim of this thesis is to create in vitro liver cancer models through organoid technology approaches, allowing for novel insights into liver cancer biology and, in turn, providing potential avenues for therapeutic testing. To model primary epithelial liver cancer cells, organoid technology is employed in part I. To study and characterize the role of ECM in liver cancer, decellularization of tumor tissue, adjacent liver tissue, and distant metastatic organs (i.e. lung and lymph node) is described, characterized, and combined with organoid technology to create improved tissue engineered models for liver cancer in part II of this thesis. Chapter 1 provides a brief introduction into the concepts of liver cancer, cellular heterogeneity, decellularization and organoid technology. It also explains the rationale behind the work presented in this thesis. In-depth analysis of organoid technology and contrasting it to different in vitro cell culture systems employed for liver cancer modeling is done in chapter 2. Reliable establishment of liver cancer organoids is crucial for advancing translational applications of organoids, such as personalized medicine. Therefore, as described in chapter 3, a multi-center analysis was performed on establishment of liver cancer organoids. This revealed a global establishment efficiency rate of 28.2% (19.3% for hepatocellular carcinoma organoids (HCCO) and 36% for cholangiocarcinoma organoids (CCAO)). Additionally, potential solutions and future perspectives for increasing establishment are provided. Liver cancer organoids consist of solely primary epithelial tumor cells. To engineer an in vitro tumor model with the possibility of immunotherapy testing, CCAO were combined with immune cells in chapter 4. Co-culture of CCAO with peripheral blood mononuclear cells and/or allogenic T cells revealed an effective anti-tumor immune response, with distinct interpatient heterogeneity. These cytotoxic effects were mediated by cell-cell contact and release of soluble factors, albeit indirect killing through soluble factors was only observed in one organoid line. Thus, this model provided a first step towards developing immunotherapy for CCA on an individual patient level. Personalized medicine success is dependent on an organoids ability to recapitulate patient tissue faithfully. Therefore, in chapter 5 a novel organoid system was created in which branching morphogenesis was induced in cholangiocyte and CCA organoids. Branching cholangiocyte organoids self-organized into tubular structures, with high similarity to primary cholangiocytes, based on single-cell sequencing and functionality. Similarly, branching CCAO obtain a different morphology in vitro more similar to primary tumors. Moreover, these branching CCAO have a higher correlation to the transcriptomic profile of patient-paired tumor tissue and an increased drug resistance to gemcitabine and cisplatin, the standard chemotherapy regimen for CCA patients in the clinic. As discussed, CCAO represent the epithelial compartment of CCA. Proliferation, invasion, and metastasis of epithelial tumor cells is highly influenced by the interaction with their cellular and extracellular environment. The remodeling of various properties of the extracellular matrix (ECM), including stiffness, composition, alignment, and integrity, influences tumor progression. In chapter 6 the alterations of the ECM in solid tumors and the translational impact of our increased understanding of these alterations is discussed. The success of ECM-related cancer therapy development requires an intimate understanding of the malignancy-induced changes to the ECM. This principle was applied to liver cancer in chapter 7, whereby through a integrative molecular and mechanical approach the dysregulation of liver cancer ECM was characterized. An optimized agitation-based decellularization protocol was established for primary liver cancer (HCC and CCA) and paired adjacent tissue (HCC-ADJ and CCA-ADJ). Novel malignancy-related ECM protein signatures were found, which were previously overlooked in liver cancer transcriptomic data. Additionally, the mechanical characteristics were probed, which revealed divergent macro- and micro-scale mechanical properties and a higher alignment of collagen in CCA. This study provided a better understanding of ECM alterations during liver cancer as well as a potential scaffold for culture of organoids. This was applied to CCA in chapter 8 by combining decellularized CCA tumor ECM and tumor-free liver ECM with CCAO to study cell-matrix interactions. Culture of CCAO in tumor ECM resulted in a transcriptome closely resembling in vivo patient tumor tissue, and was accompanied by an increase in chemo resistance. In tumor-free liver ECM, devoid of desmoplasia, CCAO initiated a desmoplastic reaction through increased collagen production. If desmoplasia was already present, distinct ECM proteins were produced by the organoids. These were tumor-related proteins associated with poor patient survival. To extend this method of studying cell-matrix interactions to a metastatic setting, lung and lymph node tissue was decellularized and recellularized with CCAO in chapter 9, as these are common locations of metastasis in CCA. Decellularization resulted in removal of cells while preserving ECM structure and protein composition, linked to tissue-specific functioning hallmarks. Recellularization revealed that lung and lymph node ECM induced different gene expression profiles in the organoids, related to cancer stem cell phenotype, cell-ECM integrin binding, and epithelial-to-mesenchymal transition. Furthermore, the metabolic activity of CCAO in lung and lymph node was significantly influenced by the metastatic location, the original characteristics of the patient tumor, and the donor of the target organ. The previously described in vitro tumor models utilized decellularized scaffolds with native structure. Decellularized ECM can also be used for creation of tissue-specific hydrogels through digestion and gelation procedures. These hydrogels were created from both porcine and human livers in chapter 10. The liver ECM-based hydrogels were used to initiate and culture healthy cholangiocyte organoids, which maintained cholangiocyte marker expression, thus providing an alternative for initiation of organoids in BME. Building upon this, in chapter 11 human liver ECM-based extracts were used in combination with a one-step microfluidic encapsulation method to produce size standardized CCAO. The established system can facilitate the reduction of size variability conventionally seen in organoid culture by providing uniform scaffolding. Encapsulated CCAO retained their stem cell phenotype and were amendable to drug screening, showing the feasibility of scalable production of CCAO for throughput drug screening approaches. Lastly, Chapter 12 provides a global discussion and future outlook on tumor tissue engineering strategies for liver cancer, using organoid technology and decellularization. Combining multiple aspects of liver cancer, both cellular and extracellular, with tissue engineering strategies provides advanced tumor models that can delineate fundamental mechanistic insights as well as provide a platform for drug screening approaches.<br/

    LIPIcs, Volume 251, ITCS 2023, Complete Volume

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    LIPIcs, Volume 251, ITCS 2023, Complete Volum

    Dissecting Extracellular Matrix Internalisation Mechanisms using Functional Genomics

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    Breast and ovarian malignancies account for one third of female cancers. The role of the stroma in supporting invasive growth in breast cancer has become clear. Breast cancer cells interact and respond to the cues from the surrounding extracellular matrix (ECM). Integrins are main cell adhesion receptors and key players in invasive migration by linking the ECM to the actin cytoskeleton. In addition, integrins mediate distinctive biochemical and biomechanical signals to support cancer invasion. The role of matrix proteases in promoting ECM degradation and cancer dissemination has been extensively studied; however, cancer cells possess additional means to support those processes, such as integrin-mediated ECM endocytosis and consequent degradation in the lysosomes. Internalisation of the extracellular matrix is upregulated in invasive breast cancer. Nonetheless, the mechanisms by which cancer cells regulate this process are poorly understood. We developed a high throughput pH sensitive system to detect ECM uptake. Here, we show that MDA-MB-231 breast cancer cells converge in macropinocytosis to internalise diverse ECM components and we confirm that this process is modulated by PAK1. To unravel which ECM components breast cancer cells internalise in a complex environment (namely, cell derived matrices), we performed mass spectrometry. Proteomic analysis identified Annexin A6, Collagen VI, Tenascin C and fibronectin, among other matrisome proteins, to be internalised by invasive breast cancer cells. Following ECM endocytosis, ECM is targeted for lysosomal degradation. To unravel the molecular mechanisms behind this process, we performed a trafficking screen and identified the AP3 complex, VAMP7, Arf1 and ARFGEF2. Our results suggest that the AP3 complex may regulate ECM-integrin delivery to lysosomes. To gain more insight on the signalling pathways governing macropinocytosis in breast cancer cells, we performed a kinase and phosphatase screen that unravelled MAP3K1 and PPP2R1A, a subunit of protein phosphatase 2A (PP2A) as relevant regulators of ECM endocytosis. Furthermore, our data suggests that p38 mitogen-activated protein kinase (MAPK) activation upon binding to the ECM is required for ECM macropinocytosis. Outstandingly, inhibiting p38 MAPK led to profound changes in the ability of breast cancer cells to migrate in cell derived matrices. Previous work from the Rainero lab focused on characterising the receptors involved in ECM internalisation; α2β1 integrin was identified as the main regulator of ECM uptake in MDA-MB-231 cells. In particular, α2β1 integrin has been shown to activate p38 MAPK pathway. Taken together, we hypothesise that binding of ECM to α2β1 integrin results in the activation of PAK1 and MAP3K1, which in turn leads to ECM endocytosis. p38 MAPK activity may induce changes in actin polymerisation via PPP2R1A and/or focal adhesion turnover, which consequently promotes ECM macropinocytosis and invasive migration

    Design of new algorithms for gene network reconstruction applied to in silico modeling of biomedical data

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    Programa de Doctorado en Biotecnología, Ingeniería y Tecnología QuímicaLínea de Investigación: Ingeniería, Ciencia de Datos y BioinformáticaClave Programa: DBICódigo Línea: 111The root causes of disease are still poorly understood. The success of current therapies is limited because persistent diseases are frequently treated based on their symptoms rather than the underlying cause of the disease. Therefore, biomedical research is experiencing a technology-driven shift to data-driven holistic approaches to better characterize the molecular mechanisms causing disease. Using omics data as an input, emerging disciplines like network biology attempt to model the relationships between biomolecules. To this effect, gene co- expression networks arise as a promising tool for deciphering the relationships between genes in large transcriptomic datasets. However, because of their low specificity and high false positive rate, they demonstrate a limited capacity to retrieve the disrupted mechanisms that lead to disease onset, progression, and maintenance. Within the context of statistical modeling, we dove deeper into the reconstruction of gene co-expression networks with the specific goal of discovering disease-specific features directly from expression data. Using ensemble techniques, which combine the results of various metrics, we were able to more precisely capture biologically significant relationships between genes. We were able to find de novo potential disease-specific features with the help of prior biological knowledge and the development of new network inference techniques. Through our different approaches, we analyzed large gene sets across multiple samples and used gene expression as a surrogate marker for the inherent biological processes, reconstructing robust gene co-expression networks that are simple to explore. By mining disease-specific gene co-expression networks we come up with a useful framework for identifying new omics-phenotype associations from conditional expression datasets.In this sense, understanding diseases from the perspective of biological network perturbations will improve personalized medicine, impacting rational biomarker discovery, patient stratification and drug design, and ultimately leading to more targeted therapies.Universidad Pablo de Olavide de Sevilla. Departamento de Deporte e Informátic

    Characterisation and State Estimation of Magnetic Soft Continuum Robots

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    Minimally invasive surgery has become more popular as it leads to less bleeding, scarring, pain, and shorter recovery time. However, this has come with counter-intuitive devices and steep surgeon learning curves. Magnetically actuated Soft Continuum Robots (SCR) have the potential to replace these devices, providing high dexterity together with the ability to conform to complex environments and safe human interactions without the cognitive burden for the clinician. Despite considerable progress in the past decade in their development, several challenges still plague SCR hindering their full realisation. This thesis aims at improving magnetically actuated SCR by addressing some of these challenges, such as material characterisation and modelling, and sensing feedback and localisation. Material characterisation for SCR is essential for understanding their behaviour and designing effective modelling and simulation strategies. In this work, the material properties of commonly employed materials in magnetically actuated SCR, such as elastic modulus, hyper-elastic model parameters, and magnetic moment were determined. Additionally, the effect these parameters have on modelling and simulating these devices was investigated. Due to the nature of magnetic actuation, localisation is of utmost importance to ensure accurate control and delivery of functionality. As such, two localisation strategies for magnetically actuated SCR were developed, one capable of estimating the full 6 degrees of freedom (DOFs) pose without any prior pose information, and another capable of accurately tracking the full 6-DOFs in real-time with positional errors lower than 4~mm. These will contribute to the development of autonomous navigation and closed-loop control of magnetically actuated SCR

    The structural and mechanical characterization of biological systems and interfaces for the study of protein misfolding diseases

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    My PhD project involved the use of high-resolution microscopy techniques to study the mechanisms driving neurodegeneration in protein aggregation diseases, and to investigate the effects of anti-aggregation drugs. Several pieces of evidence indicate that in neurodegenerative diseases, such as Alzheimer’s and Parkinson’s diseases, toxic behaviour could result from the action of amyloid aggregates. The latter are highly organized and insoluble aggregates that are formed upon misfolding and aggregation of soluble proteins which undergo destabilization of their native structure. These proteins share the common characteristic of aggregating into fibrillar structures, referred to as "amyloid fibrils" with a high content of β-sheets and specific cross-beta arrangement. The study was conducted using advanced atomic force microscopy (AFM) both as a single technique to mechanistically and structurally characterize biological systems and interfaces involved in the interaction with toxic protein aggregates (through imaging and analysis of force/distance curves), and as a combined technique, together with optical microscopy, to understand the molecular mechanisms of protein aggregation, which represents a crucial problem to counteract misfolded protein diseases

    Étude de la relation entre la transcription et la structure de riborégulateurs répondant à la thiamine pyrophosphate chez Escherichia coli

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    Dans cet ouvrage, l’étude de la relation entre la transcription et la structure de riborégulateurs répondant à la thiamine pyrophosphate chez Escherichia coli est décrite. Par des expériences de cinétique de transcription employant le facteur de transcription NusA et couplées à des expériences de mutagenèse dirigée, une structure de type tige-boucle induisant une augmentation de la demi-vie apparente de deux pauses transcriptionnelles dans le riborégulateur thiC a été découverte. Par la suite, la présence de structures similaires situées près du codon d’initiation des riborégulateurs tbpA, thiM, lysC et btuB a été investiguée par des méthodes similaires. Les résultats suggèrent la présence de tige-boucles induisant une augmentation des pauses près du codon d’initiation de ces riborégulateurs, mais des expériences supplémentaires seront nécessaires pour la confirmer. Afin de nous aider dans l’étude des systèmes comportant plusieurs pauses consécutives, l’utilisation du 6-nitropiperonyloxyméthyl (NPOM), une modification chimique de l’ADN agissant comme barrage transcriptionnel amovible, a été développée. Le NPOM a ensuite été utilisé pour étudier les deux pauses du riborégulateur thiC qui sont influencées par la tige-boucle en amont de la première et déterminer que l’effet apparent sur la seconde pause est seulement dû à la première pause, qui désynchronise les complexes transcriptionnels. Finalement, le développement de méthodes de production de complexes transcriptionnels marqués avec des fluorophores, dans un but d’étude à l’appareillage d’observation de molécule uniques, est discuté. Premièrement, de l’ADN marqué avec deux fluorophores et faisant partie d’un complexe transcriptionnel lié à une lame de miscroscope via l’ARN a été utilisé pour faire une preuve de concept utilisant la perte de signal de ces fluorophores pour mesurer le temps requis pour transcrire un riborégulateur.. Deuxièmement, la production de complexes transcriptionnels dont l’ARN est doublement marqué à des endroits spécifiques avec des fluorophores est discutée. Les méthodes employées, incluant une combinaison de transcriptions par étapes, d’incorporations de nucléotides non naturels dans l’ARN, de réactions chimiques spécifiques entre un groupement azoture et un DBCO ou un alcyne, ont donné des résultats variables, mais qui ont permis d’infirmer plusieurs hypothèses, en plus de produire un complexe transcriptionnel dont l’ARN est doublement marqué pour la première fois au laboratoire. Cela étant dit, l’utilisation du NPOM pour transcrire sur de longues distances a permis de marquer spécifiquement l’ARN à des positions jusqu’ici inaccessibles, ouvrant la voie à l’étude de l’ARN natif impliquant des marquages éloignés du site de départ de la transcription
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