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Qiao, Yi. "Tumor subclone structure reconstruction with genomic variation data." Thesis, Boston College, 2014. http://hdl.handle.net/2345/bc-ir:104182.
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Thesis advisor: Gabor MarthUnlike normal tissue cells, which contain identical copies of the same genome, tumors are composed of genetically divergent cell subpopulations, or subclones. The abilities to identify the number of subclones, their frequencies within the tumor mass, and the evolutionary relationships among them are crucial in understanding the basis of tumorigenesis, drug response, relapse, and metastasis. It is also essential information for informed, personalized therapeutic decisions. Studies have attempted to reconstruct subclone structure by identifying distinct allele frequency distribution modes at a handful of somatic single nucleotide variant loci, but this question was not adequately addressed with computational means at the start of this dissertation work, and recent efforts either enforce certain assumptions or resort to statistical procedure which cannot guarantee the complete landscape of solution space. This dissertation present a computational framework that examines somatic variation events, such as copy number changes, loss of heterozygosity, or point mutations, in order to identify the underlying subclone structure. Chapter 2 discuss the presence of intra-tumoral heterogeneity, and for historical interest, a method to reconstruct the parsimonious solution based on simplifying assumptions in tumor micro-evolution process. Analysis results on clinical datasets concerning Ovarian Serious Carcinoma and Intracranal Germ Cell Tumor based on this method, which confirmed the genomic complexity, are also presented. Due to the reason that the linkage information i.e. whether two mutations are co-localizing in the same cancer cell is lost during tissue homogenization and DNA fragmentation, common sample preparation steps used in whole genome profiling techniques, often there are more than one subclone model capable of explaining the observation. Chapter 3 describes an extended method that is able to search for all models consistent with the observation. Consequently, the solution to a specific input dataset is then a set of possible subclone structures. The method then trim this solution space in the case that more than one sample from the same patient are available, such as the primary and relapse tumor pairs. Furthermore, a statistical framework is developed that, when further trimming is not possible, predicts whether two mutations are co-localizing in the same subclone. The formal definition on the problem of subclone structure reconstruction, as well as techniques to pre-process various types of genomic variation data are given given here as well. Results on the analysis of published and novel datasets, ranging from cancer types including Acute Myeloid Leukemia, Sinonasal Undifferenciated Carcinoma and Ovarian Serious Carcinoma, and data types including whole genome sequencing, copy number array, single nucleotide polymorphism array and single nucleotide variant calls with deep sequencing are also included. They show that the method is applicable to these wide range of cancer and data types, able to independently replicate the published conclusion based on manual reasoning, and gain novel insights into the pattern of tumor recurrence and chemoresistance. It also shows that the method can be valuable in prioritizing variants for function study
Thesis (PhD) — Boston College, 2014
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
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Srinivasan, Seetha V. "Loss of the RB tumor suppressor contributes to genomic instability." Cincinnati, Ohio : University of Cincinnati, 2002. http://rave.ohiolink.edu/etdc/view.cgi?acc_num=ucin1212166350.
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Thesis (Ph.D.)--University of Cincinnati, 2008.Advisor: Erik S. Knudsen. Title from electronic thesis title page (viewed Sep. 8, 2008). Keywords: RB; cell cycle; DNA replication; mitosis; p53; ploidy; genome integrity. Includes abstract. Includes bibliographical references.
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SRINIVASAN, SEETHA V. "Loss of the RB tumor suppressor contributes to genomic instability." University of Cincinnati / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1212166350.
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Barbee, Bonnie. "Genomic Heterogeneity of Glioblastoma: A Comparison of the Enhancing Tumor Core and the Brain Around the Tumor." Thesis, The University of Arizona, 2016. http://hdl.handle.net/10150/603560.
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Holcomb, Ilona Noelani. "Genomic profiling of prostate cancer within and beyond the primary tumor /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/10282.
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Rooney, Michael Steven. "Integrative genomic approaches to dissecting host-tumor and host-pathogen immune processes." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/98722.
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Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2015.Cataloged from PDF version of thesis.
Includes bibliographical references (pages 243-263).
Two parallel research efforts were pursued. First, we conducted a systematic exploration of how the genomic landscape of cancer shapes and is shaped by anti-tumor immunity. Using large-scale genomic data sets of solid tissue tumor biopsies, we quantified the cytolytic activity of the local immune infiltrate and identified associated properties across 18 tumor types. The number of predicted MHC Class I-associated neoantigens was correlated with cytolytic activity and was lower than expected in colorectal and other tumors, suggesting immune-mediated elimination. We identified recurrently mutated genes that showed positive association with cytolytic activity, including beta-2- microglobulin (B2M), HLA-A, -B and -C and Caspase 8 (CASP8), highlighting loss of antigen presentation and blockade of extrinsic apoptosis as key strategies of resistance to cytolytic activity. Genetic amplifications were also associated with high cytolytic activity, including immunosuppressive factors such as PDL1/2 and ALOX12B/15B. Our genetic findings thus provide evidence for immunoediting in tumors and uncover mechanisms of tumor-intrinsic resistance to cytolytic activity. Second, we combined measurements of protein production and degradation and mRNA dynamics so as to build a quantitative genomic model of the differential regulation of gene expression in lipopolysaccharide-stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for more than half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction for newly activated cellular functions and by protein lifecycle changes for remodeling of preexisting functions.
by Michael Steven Rooney.
Ph. D.
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Fishler, Kristen B. S. "“It’s the Wild, Wild West Out There” Experiences of a Multidisciplinary Genomic Breast Cancer Tumor Board Implementing Tumor Sequencing in Clinical Care." University of Cincinnati / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1525169475571341.
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O'Connor, Brian Daniel. "Analysis of high level patterns in genomic data from protein thermostability to tumor biology /." Diss., Restricted to subscribing institutions, 2007. http://proquest.umi.com/pqdweb?did=1383484301&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.
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Pereira, Carolina Ruivo 1986. "Genomic profile of tumorgrafts identifies B2M as a novel tumor suppressor gene in lung cancer." Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/482055.
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El cáncer de pulmón es la forma más mortal de cáncer en el mundo. Recientemente, el estudio del perfil genómico a larga escala de tumores humanos ha impulsado el desarrollo de drogas que tienen como diana terapéutica genes alterados. Dado que las terapias dirigidas son escasas, el descubrimiento de nuevos genes implicados en cáncer de pulmón con relevancia clínica es crucial.
Por eso, este proyecto tuvo como base la secuenciación de exomas y transcriptomas de xenotransplantes de pulmón. La pureza tumoral alcanzada durante el injerto fue fundamental, sobre todo para identificar delecciones homocigóticas y amplificaciones génicas. El gen B2M (β2-microglobulina), encontrado inactivado en 5% de los tumores pulmonares, se caracterizó. Su pérdida genética se correlacionó con bajos niveles de infiltración intratumoral por linfocitos T citotóxicos. Además, la β2-microglobulina se asoció a supervivencia en pacientes tratados con agentes anti-PD1/PD-L1, evidenciando su rol potencial el predecir respuestas a inmunoterapias en neoplasias pulmonares.Lung cancer is the deadliest form of cancer worldwide. Recently, the large-scale genomic profiling of human tumors has fueled the development of efficient anticancer agents that target the activity of mutated genes. Given that directed therapies are still very scarce, the discovery of novel lung cancer-related genes with potential relevance within the clinical context is imperative. Thus, this project consisted on coupling high-throughput sequencing strategies (exomes and transcriptomes) with the use of lung tumorgrafts. The high tumor purity achieved through the engraftment was crucial, particularly to identify homozygous deletions and gene amplifications. The B2M gene (β2-microglobulin), found to be mutated in 5% of lung tumors, was characterized. Its genetic loss was correlated to lower cytotoxic T-cell intratumoral infiltration, probably impairing the immune-mediated tumor eradication. Moreover, β2-microglobulin was associated with survival in patients treated with anti-PD-1/PD-L1 agents, highlighting a potential role in predicting response to immunologically-based therapies in lung cancer.
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Patrick, James Lambert. "Computer Aided Analysis of Restriction Landmark Genomic Scanning Images from Tumor and Cell Line Models." University of Toledo Health Science Campus / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=mco1196365469.
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Wong, Pak Cheung Ronald. "The role of tumor suppressor Inhibitor of Growth 1 in lesion bypass pathway and genomic stability." Thesis, University of British Columbia, 2011. http://hdl.handle.net/2429/37894.
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The lesion bypass pathway, which is regulated by monoubiquitination of proliferating cell nuclear antigen (PCNA), is essential for resolving replication stalling due to DNA lesions. This process is important for preventing genomic instability and cancer development. In this thesis, I demonstrated a novel tumor suppressor function of p33ING1 (ING1b) in preserving genomic stability upon replication stress through regulating PCNA monoubiquitination. We found that ING1b knockdown cells are more sensitive to UV due to defects in recovering from UV-induced replication blockage, leading to enhanced genomic instability. We revealed that ING1b is required for the E3 ligase Rad18-mediated PCNA monoubiquitination in lesion bypass. Interestingly, ING1b-mediated PCNA monoubiquitination is associated with the regulation of histone H4 acetylation. For the first time, we have shown that chromatin remodeling contributes to the stabilization of stalled replication fork and to the regulation of PCNA monoubiquitination during lesion bypass.
Previously, our group showed that ING1b is phosphorylated by the S phase checkpoint kinase Chk1 at S126 residue. We further showed that ING1b cooperated with Chk1 in maintaining genomic stability. We found that ING1b interacted with Chk1 after UV through ING1b S126 residue. Furthermore, we found that ING1b S126 residue was required for PCNA monoubiquitination, Pol-eta foci and therefore preventing chromosomal aberrations after UV. These data suggest that ING1b cooperates with Chk1 through the S126 residue in mediating PCNA monoubiquitination, lesion bypass and genomic stability.
We further explored the role of the E3 ligase Rad18, a key regulator for the lesion bypass pathway, in melanoma using melanoma tissue microarray. We found that Rad18 expression was significantly upregulated in melanoma. Strong Rad18 expression correlated with worse 5-year patient survival in the sun-protected sites. Interestingly, we found an opposite role of Rad18 on patient survival in the sun-exposed sites. Furthermore, we showed that melanoma cell proliferation and the expression of pAkt and cyclin D1 were reduced upon Rad18 knockdown.
The work presented in this thesis leads to a better understanding of the role of ING1b and lesion bypass pathway in genomic stability and melanoma development. It has implications on designing new strategies for cancer therapy.
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Neville, Matt J. "Characterisation of the genomic region around the TNF locus within the human major histocompatibility complex in the chromosome band 6p21.3." Thesis, University of Oxford, 2000. http://ora.ox.ac.uk/objects/uuid:1fcb0019-0b54-418a-a44c-b1b4a7d5a51e.
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It is becoming increasingly apparent that many of the genes in the class III region of the human Major Histocompatibility Complex encode proteins involved in the immune and inflammatory responses. Furthermore, genetic studies have indicated that genes within the class III region, particularly the telomeric segment containing the TNF gene, could contribute to susceptibility to diseases of immune-related aetiology. To further characterise this region and to identify candidate disease susceptibility genes, two overlapping cosmids, TN62 and TN82, covering an ~82kb segment of DNA around the TNF gene were selected for sequence analysis. The eight known genes in this region have been precisely positioned with the order: Gl/AIF-1, 1C7, LST1 (B144), LTB, TNF, LTA, IKBL, BAT1 (centromere to telomere) and their genomic structures have been defined. Comparison of the Gl genomic region with previously described cDNA and genomic sequences, together with the results of RT-PCR, indicates that three alternative transcripts, Gl, Allograft Inflammatory Factor-1 and Interferon-γ Responsive Transcript-1, are all derived from this gene. The completion of the sequence of 1C7 (D6S2570) has revealed that this gene encodes a putative novel member of the immunoglobulin superfamily. A number of alternatively spliced transcripts of 1C7 were identified by RT-PCR, all of which are expressed in immune-related cell lines. Alternative splicing within the immunoglobulin domain- encoding region was seen to result in possible set switching between an IgV domain and an IgC2 domain. In addition to this, a previously unidentified gene, homologous to a number of V- ATPase G-subunits, has been located 1kb telomeric of IKBL. Lastly, the pseudogene UCRH-L and an AIF-1 gene fragment have been identified in the intergenic region between AIF-1 and 1C7. In order to assess the contribution of loci in this region to disease susceptibility, the genes AIF-1, 1C7, ATP6G and the BAT1 promoter region were subjected to mutation analysis. A total of 28 polymorphisms have been identified, 8 in AIF-1, 10 in 1C7, 7 in ATP6G and 3 in the BAT1 promoter region. Work is at present underway to genotype a number of the identified polymorphisms in control DNAs and in DNA samples from patients with combined variable immunodeficiency (CVID). The information generated from this analysis will bring us closer to explaining the reported linkage of CVID with the telomeric end of the human MHC class III region.
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Hamm, Christopher Allan. "Functional genomic analyses of the impact of global hypomethylation and of tumor microenvironment in a rat model of human chondrosarcoma." Diss., University of Iowa, 2009. https://ir.uiowa.edu/etd/372.
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Chondrosarcomas are malignant cartilage tumors that do not respond to traditional chemotherapy or radiation. The 5-year survival rate of histologic grade III chondrosarcoma is less than 30%. To achieve a greater understanding of chondrosarcoma tumorigenesis, a model for human chondrosarcoma has been established in a rat system. The model, known as the Swarm rat chondrosarcoma (SRC), resembles human chondrosarcoma and provides a system to study tumor growth and progression. Here we examined the influence of the tumor microenvironment and the impact of genome-wide hypomethylation on the behavior of SRC tumors, two factors known to contribute fundamentally to the development and progression of solid tumors.
Previous studies with SRC revealed that tumor microenvironment can significantly influence chondrosarcoma malignancy, but the underlying biologic mechanisms have not been defined. To address this issue we carried out epigenetic and gene expression studies on the SRC tumors that were initiated at different transplantation sites. The epigenetic analysis revealed that microenvironmental changes could promote global DNA hypomethylation in SRC cells. Subsequent gene expression analyses revealed that the transplantation site had a significant impact on the gene expression profiles of SRC tumors. These SRC tumors had unique gene expression profiles, and we were able to identify genes that were differentially expressed between SRC tumors originating from different transplantation sites. Functional analyses of two differentially expressed genes, thymosin-beta-4 and c-fos, provided insight into the role that these genes may play in the development and progression of chondrosarcoma.
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Burrows, Anna. "Genome-Wide Loss-of-Function Genetic Screens Identify Novel Senescence Genes and Putative Tumor Suppressors." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10191.
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During every cell cycle and upon exogenous stress, tumor suppression programs are engaged to ensure genomic stability. In response to replicative aging and oncogenic stimuli, the p53 and Rb pathways are activated to prevent the proliferation of damaged cells. Several lines of evidence suggest that escape from senescence is a crucial early step in oncogenic progression. A major challenge in the cancer field is to combine genomic information regarding cancer-associated genetic changes with high-throughput functional studies, in order to confirm genetic requirements and pinpoint biological roles of these perturbed genes in oncogenesis. Furthermore, a complete genetic understanding of replicative senescence, and how it might be bypassed, is lacking. We describe here two genome scale loss-of-function genetic screens that interrogate these tumor suppressor programs. We utilized a unique sensitization approach to isolate senescence pathways and unmask compensatory mechanisms that may have been difficult to identify in previous studies. These genetic screens have generated comprehensive and validated datasets of putative senescence and p53 pathway genes. We present this dataset as a high-quality resource for further investigation into these biological pathways. We have uncovered several genes in distinct biological pathways which have not been demonstrated to have a functional role in senescence, and which may be putative tumor suppressors. We have identified BRD7 and BAF180, two SWI/SNF components, as critical regulators of p53. BRD7 and BAF180 are required for p53 activity and p21 expression during replicative and oncogene-induced senescence, and evidence suggests that they are inactivated in human cancer. In addition, we have uncovered a role for the deubiquitinating enzyme USP28 in the regulation of p53 accumulation during senescence, such that loss of USP28 results in bypass of the senescence program. We have also investigated several other novel senescence genes including SEMA6A, SEMA3b, and TMEM154. We have found that the expression of these genes is highly regulated during senescence by distinct means, including both p53-dependent and p53-independent mechanisms. These results demonstrate the efficacy of our sensitized screening approach, and also highlight the emerging view that the senescence program requires the combined action of multiple biological pathways for its execution.
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Benetkiewicz, Magdalena. "Development and Application of Human Chromosome 22 Genomic Microarray : Chromosome 22-Associated Disorders Analyzed by Array-Based Comparative Genomic Hybridization." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6272.
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Nord, Helena. "Application of Genomic and Expression Arrays for Identification of new Cancer Genes." Doctoral thesis, Uppsala universitet, Genomik, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-121957.
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Copy number variation (CNV) comprises a recently discovered kind of variation involving deletion and duplication of DNA segments of variable size, ranging from a few hundred basepairs to several million. By altering gene dosage levels or disrupting proximal or distant regulatory elements CNVs create human diversity. They represent also an important factor in human evolution and play a role in many disorders including cancer. Array-based comparative genomic hybridization as well as expression arrays are powerful and suitable methods for determination of copy number variations or gene expression changes in the human genome. In paper I we established a 32K clone-based genomic array, covering 99% of the current assembly of the human genome with high resolution and applied it in the profiling of 71 healthy individuals from three ethnic groups. Novel and previously reported CNVs, involving ~3.5% of the genome, were identified. Interestingly, 87% of the detected CNV regions overlapped with known genes indicating that they probably have phenotypic consequences. In papers II through IV we applied this platform to different tumor types, namely two collections of brain tumors, glioblastoma (paper II) and medulloblastoma (paper III), and a set of bladder carcinoma (paper IV) to identify chromosomal alterations at the level of DNA copy number that could be related to tumor initiation/progression. Tumors of the central nervous system represent a heterogeneous group of both benign and malignant neoplasms that affect both children and adults. Glioblastoma and medulloblastoma are two malignant forms. Glioblastoma often affects adults while the embryonal tumor medulloblastoma is the most common malignant brain tumor among children. The detailed profiling of 78 glioblastomas, allowed us to identify a complex pattern of aberrations including frequent and high copy number amplicons (detected in 79% of samples) as well as a number of homozygously deleted loci. These regions encompassed not only previously reported oncogenes and tumor suppressor genes but also numerous novel genes. In paper III, a subset of 26 medulloblastomas was analyzed using the same genomic array. We observed that alterations involving chromosome 17, especially isochromosome 17q, were the most common genomic aberrations in this tumor type, but copy number alterations involving other chromosomes: 1, 7 and 8 were also frequent. Focal amplifications, on chromosome 1 and 3, not previously described, were also detected. These loci may encompass novel genes involved in medulloblastoma development. In paper IV we examined for the presence of DNA copy number alterations and their effect on gene expression in a subset of 21 well-characterized Ta bladder carcinomas, selected for the presence or absence of recurrences. We identified a number of novel genes as well as a significant association between amplifications and high-grade and recurrent tumors which might be clinically useful. The results derived from these studies increase our understanding of the genetic alterations leading to the development of these tumor forms and point out candidate genes that may be used in future as targets for new diagnostic and therapeutic strategies.
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Zer, Cindy. "The genomic targets of p38 mitogen activated protein kinase mediating tumor necrosis factor alpha signaling in fribroblast-like synoviocytes." Diss., Restricted to subscribing institutions, 2008. http://proquest.umi.com/pqdweb?did=1692114531&sid=3&Fmt=2&clientId=1564&RQT=309&VName=PQD.
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Kunkle, Brian W. "The Potential Role of Environmental Exposures and Genomic Signaling in Development of Central Nervous System Tumors." FIU Digital Commons, 2011. http://digitalcommons.fiu.edu/etd/524.
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The etiology of central nervous system tumors (CNSTs) is mainly unknown. Aside from extremely rare genetic conditions, such as neurofibromatosis and tuberous sclerosis, the only unequivocally identified risk factor is exposure to ionizing radiation, and this explains only a very small fraction of cases. Using meta-analysis, gene networking and bioinformatics methods, this dissertation explored the hypothesis that environmental exposures produce genetic and epigenetic alterations that may be involved in the etiology of CNSTs.
A meta-analysis of epidemiological studies of pesticides and pediatric brain tumors revealed a significantly increased risk of brain tumors among children whose mothers had farm-related exposures during pregnancy. A dose response was recognized when this risk estimate was compared to those for risk of brain tumors from maternal exposure to non-agricultural pesticides during pregnancy, and risk of brain tumors among children exposed to agricultural activities. Through meta-analysis of several microarray studies which compared normal tissue to astrocytomas, we were able to identify a list of 554 genes which were differentially expressed in the majority of astrocytomas. Many of these genes have in fact been implicated in development of astrocytoma, including EGFR, HIF-1α, c-Myc, WNT5A, and IDH3A. Reverse engineering of these 554 genes using Bayesian network analysis produced a gene network for each grade of astrocytoma (Grade I-IV), and ‘key genes’ within each grade were identified. Genes found to be most influential to development of the highest grade of astrocytoma, Glioblastoma multiforme (GBM) were: COL4A1, EGFR, BTF3, MPP2, RAB31, CDK4, CD99, ANXA2, TOP2A, and SERBP1. Lastly, bioinformatics analysis of environmental databases and curated published results on GBM was able to identify numerous potential pathways and gene-environment interactions that may play key roles in astrocytoma development.
Findings from this research have strong potential to advance our understanding of the etiology and susceptibility to CNSTs. Validation of our 'key genes' and pathways could potentially lead to useful tools for early detection and novel therapeutic options for these tumors.
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Hamm, Christopher Allan Soares Marcelo B. "Functional genomic analyses of the impact of global hypomethylation and of tumor microenvironment in a rat model of human chondrosarcoma." [Iowa City, Iowa] : University of Iowa, 2009. http://ir.uiowa.edu/etd/372.
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Weber, Zachary Thomas. "Applications of ctDNA Genomic Profiling to Metastatic Triple Negative Breast Cancer." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1586787923790178.
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Palau, de Miguel Montserrat. "Detection of Helicobacter pylori Microevolution and Multiple Infection, and Genomic Analysis of Helicobacter pylori Strains." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/668148.
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In the past decades, Helicobacter pylori has received the attention of many researchers because of its known relation with gastric cancer. Although many studies have tried to decipher the exact relation between the bacteria and cancer state, and several virulence factors have been discovered, an exact answer has not been found yet. Further work should be made in order to study more accurately the genome of this bacterium and to understand its precise involvement. The bacterium is characterised for a highly genetic diversity, meaning it is continuously changing in order to adapt itself to its hostile niche, the human stomach.
Infection by H. pylori is estimated to affect half of the world’s population, being more extended in developing countries than in developed ones, possibly due to the high consumption of antibiotics and the increased level of sanitation in the latest. It has been demonstrated that the gastric lumen can be colonized by more than just one strain of the bacterium, sometimes these strains could have evolved from the same ‘mother’ strain, or they could come from unrelated strains. The study of these situations is important in order to elucidate if there is just one strain who is responsible for starting the pathogenic cascade, and what are the specific differences between the different strains that inhabit the human stomach.
On the first work of this thesis, our group studied the usefulness of six housekeeping genes for the detection of H. pylori infection and the characterization of various strains isolated from gastric isolates, studying as well their phylogeny. In some cases, the distance value between the strains was high, indicating and event of multiple infection. In other cases, small differences were found between clones, suggesting events of microevolution rather than multiple infection.
This work was further extended with the study of the usefulness of amplicon sequencing of these housekeeping genes in the detection of microevolution and mixed infections from gastric biopsies of patients with dyspeptic symptoms and different histopathological findings (from atrophy to adenocarcinoma). Five gastric biopsies from four patients infected by H. pylori were involved in this study. We detected in all the analyzed gastric biopsies multiple H. pylori infections with a predominant strain. These results suggest that H. pylori colonizes the human stomach through diverse infection circumstances that lead to a gastric multi-infection with a predominant strain together alongside other minority strains. Furthermore, it was shown that mixed infections are the main status in the colonization of the human gastric mucosa.
The last part of this thesis started with a preliminary study of 51 complete sequenced
H. pylori genomes and further focused on three genomes obtained from the same patient in order to analyse and compare them. Particularly, these isolates were sampled at the same time from a stomach with adenocarcinoma, one strain was from the non- tumoral tissue, and the other two were isolated from the tumoral tissue. They all lacked from the most noticeable virulence factor, the cag pathogenicity island; one of the most studied and the main factor related to the malignancy of the bacterium. On the other hand, we found differences in the genotype of the vacuolating cytotoxin gene (vacA) and in genes related with urease, the outer membrane and flagella.
Despite the contributions made in this thesis, further studies are needed to find better genetic markers of H. pylori related to virulence and progression to gastric cancer.Helicobacter pylori és el focus d’atenció de molts estudis a causa de la seva coneguda relació amb el càncer gàstric. Encara que molts estudis han tractat de desxifrar la relació exacta entre el bacteri i la progressió del càncer, i s'han descobert diversos factors de virulència, no s'ha trobat una resposta exacta. En la primera part d'aquesta tesi, es va estudiar la utilitat de sis gens conservats per la detecció de la infecció per H. pylori i la caracterització de diverses soques aïllades de biòpsies gàstriques, estudiant-se també la seva filogènia. En alguns casos, el valor de la distància entre les soques era alt, fet indicatiu d’un esdeveniment d'infecció múltiple. En altres casos, es van trobar petites diferències entre els clons, el que suggereix esdeveniments de microevolució en lloc d’infecció múltiple. Aquesta tesi es va ampliar amb l'estudi de la utilitat de la seqüenciació d'amplicons d'aquests gens conservats en la detecció de microevolució i infeccions múltiples en biòpsies gàstriques de pacients amb símptomes dispèptics. En aquest estudi es van analitzar cinc biòpsies gàstriques de quatre pacients infectats per H. pylori. En totes les biòpsies gàstriques analitzades es van detectar infeccions múltiples per H. pylori amb una soca predominant. Aquests resultats suggereixen que H. pylori colonitza l'estómac humà mitjançant diverses circumstàncies d'infecció que condueixen a una infecció múltiple gàstrica amb una soca predominant juntament amb altres soques minoritàries. L'última part d'aquesta tesi va començar amb l’estudi preliminar de 51 genomes complets d’H. pylori i es va centrar després en l’estudi i comparació de tres genomes obtinguts del mateix pacient. Específicament, aquestes soques van ser aïllades alhora d’un estómac amb adenocarcinoma, on una soca provenia del teixit no tumoral i les altres dues del teixit tumoral. Totes mancaven del factor de virulència més destacat, l'illa de patogenicitat cag; un dels factors més estudiats i el més relacionat amb la malignitat del bacteri. Per una altra banda, vam trobar diferències en el genotip del gen vacA i en gens relacionats amb la ureasa, la membrana externa i els flagels.
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Blegen, Harald. "Genomic instability and tumor progression : a cytochemical, molecular biological and cytogenetic study of human tissue from uterine cervix, colon, breast and ovary /." Stockholm, 1999. http://diss.kib.ki.se/1999/91-628-3464-9/.
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Rodríguez, Sodupe Pau 1993. "Liquid biopsy for early tumor relapse detection : Development of hypersensitive genomic sequencing methodologies for the detection of ultra-rare genetic variants in the blood plasma of pediatric cancer patients." Doctoral thesis, TDX (Tesis Doctorals en Xarxa), 2022. http://hdl.handle.net/10803/673741.
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The profiling of circulating-tumor DNA (ctDNA) in blood plasma, often known as liquid biopsy, has recently
been of great interest in cancer research. This minimally-invasive strategy relies on the fact that ctDNA
represents, at least partially, the real-time state of the tumor genome and holds great potential for early
cancer detection and patient care. However, the fraction of ctDNA in total cell-free DNA (cfDNA) is often very
low and requires ultra-sensitive and specific methods for its detection. This thesis focuses on the
development and implementation of ultra-sensitive Next Generation Sequencing (NGS) methods that enable
the identification of rare variants in plasma in a specific way. In summary, this work presents a
comprehensive and cost-effective strategy for monitoring tumor mutations in the plasma of pediatric patients
in a personalized manner. Our strategy aims to provide a tool to anticipate the detection and treatment of
tumor relapses.L’anàlisi d'ADN tumoral circulant (ADNtc) al plasma sanguini, sovint conegut com a biòpsia líquida, ha despertat recentment gran interès en la recerca del càncer. Aquesta estratègia mínimament invasiva es basa en que l’ADNtc representa, almenys parcialment, l'estat en temps real del genoma del tumor i té un gran potencial per a la detecció precoç del càncer. Tanmateix, la fracció d'ADNct en l'ADN lliure circulant (ADNlc) total és sovint molt baixa i es requereixen mètodes ultra-sensibles i específics per a la seva detecció. Aquesta tesi se centra en el desenvolupament i la implementació de mètodes ultra-sensibles basats en tecnologies de seqüenciació massiva (NGS) que permetin la identificació de variants rares en plasma de forma específica. En resum, aquest treball presenta una estratègia integral i rendible pel seguiment de mutacions tumorals en el plasma de pacients pediàtrics de manera personalitzada. La nostra estrategia pretén oferir una eina que permeti anticiparse en la detecció i tractament de recidives tumorals.
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Balakrishnan, Subhasree. "Ets2 and Pten regulate ErbB2-driven mammary tumorigenesis from stromal fibroblasts." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1458944094.
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La, Bella Tiziana. "Adeno-associated virus in the liver : natural history of the infection and consequences in tumor development." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCC263.
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Le virus adéno-associé (AAV) est un virus à ADN monobrin, défectif et endémique dans la population humaine. L'infection à AAV a longtemps été considérée comme non pathogénique. Cependant, il y a quelques années, nous avons identifié pour la première fois des insertions clonales récurrentes d'AAV2 impliquées dans la pathogenèse du carcinome hépatocellulaire humain (CHC) développé sur un foie normal. Ces insertions virales clonales ciblent des oncogènes et entraînent leur surexpression. À ce jour, peu de travaux ont étudié l'infection à AAV de type sauvage dans le foie humain. Dans ce travail, nous avons étudié l'histoire naturelle de l'infection virale dans les tissus hépatiques et ses conséquences sur le développement de tumeurs dans une vaste cohorte de patients (n = 1464). La présence de l'AAV est observée chez 21% des patients, plus fréquemment dans la contrepartie non-tumorale (18%) que dans la tumeur (8%) et significativement enrichie chez les femmes, les patients jeunes et non cirrhotiques. Deux sous-types d’AAV ont été identifiés dans le foie, l’AAV2 classique et un génotype hybride AAV2-AAV3-AAV13, avec une fréquence égale dans notre cohorte. Nous avons détecté la présence de formes épisomales d'AAV dans 27% des tissus non tumoraux positifs pour l'AAV, associée de manière significative à l'expression de l'ARN viral et à la co-infection par des virus auxiliaires, suggérant une infection active en cours. Nous avons identifié le virus de l'herpès humain de type 6 (HHV6) comme étant le virus auxiliaire naturel de l'AAV dans le foie. En revanche, l'ADN de l'adénovirus n'a été détecté que chez 0,5% des patients et aucune association avec l'AAV n'a été constatée. Nous avons confirmé la sélection positive des insertions d'AAV clonales au cours du développement du CHC chez les patients sans cirrhose dans 2% des tumeurs ciblant CCNA2, CCNE1, TERT, TNFSF10, KMT2B et INHBE / GLI1. De plus, les altérations de CCNA2 et de CCNE1 dues à des insertions virales d'AAV et de VHB ou à des réarrangements structurels ont défini une nouvelle sous-classe de CHC (CCN-HCC) et un nouveau mécanisme de développement du CHC sur le foie normal, améliorant nos connaissances sur l'hépatocarcinogénèse sur le foie non cirrhotique. Les CCN-HCC présentent également des caractéristiques moléculaires particulières qui pourraient être ciblées par un traitement spécifiqueAdeno-associated virus (AAV) is a defective mono-stranded DNA virus, endemic in human population. AAV infection has long been considered as non-pathogenic, however few years ago we reported for the first time recurrent clonal AAV2 insertion in the pathogenesis of human hepatocellular carcinoma (HCC) developed on normal liver. These clonal viral insertions target cancer driver genes leading to their overexpression. To date, little is known about wild type AAV infection in human liver. In this work we investigated the natural history of the viral infection in the liver tissues and the consequences in tumor development in a large cohort of patients (n=1464). The presence of AAV was observed in 21% of patients, more frequently in the non-tumor counterpart (18%) than in tumor (8%) and significantly enriched in young, female and non-cirrhotic patients. Two AAV subtypes were identified in the liver, the classical AAV2 and a hybrid AAV2-AAV3-AAV13 genotypes, with an equal frequency in our cohort. We detected the presence of episomal AAV forms in 27% of AAV positive non-tumor tissues significantly associated with viral RNA expression and co-infection with helper viruses suggesting an ongoing active infection. We identified human herpes virus type 6 (HHV6) as the natural AAV helper virus in the liver. In contrast, adenovirus DNA was detected in only 0.5% of patients and no association with AAV was found. We confirmed the positive selection of clonal AAV insertions during HCC development in patients without cirrhosis in 2% of tumors targeting CCNA2, CCNE1, TERT, TNFSF10, KMT2B and INHBE/GLI1. Moreover, the alterations in CCNA2 and CCNE1 due to viral insertions of AAV and HBV or structural rearrangements defined a new subclass of HCCs (CCN-HCC) and a novel mechanism of HCC development on normal liver improving our knowledge on hepatocarcinogenesis on non-cirrhotic liver. CCN-HCCs display also peculiar molecular features that could be targeted by specific treatment
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Abbou, Samuel. "Liquid Biopsy in Pediatric Sarcoma." Thesis, université Paris-Saclay, 2022. http://www.theses.fr/2022UPASL037.
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Résumé : Les biopsies liquides ouvrent de nouveaux champs d'applications dans la prise en charge des patients au diagnostic, au cours de leur suivi et également en recherche translationnelle. Ces dernières années, de nombreux efforts ont été consacrés au développement de l'ADN tumoral circulant (ADNct) et des cellules tumorales circulantes (CTC). Il y a malgré tout de nombreux terrains encore en friches dans les cancers de l'enfant, et parmi eux dans les sarcomes pédiatriques.Nous avons souhaité explorer dans ce travail différents aspects des applications cliniques éventuelles et d'utilisation de ces technologies pour la compréhension de la biologie des tumeurs. La première partie de ce projet est une revue de la littérature qui se rapporte à l'application de l'ADNct dans les cancers solides pédiatriques. Nous présentons ensuite un travail de recherche qui vise à utiliser les CTC à visée diagnostique dans les sarcomes à translocation. Cette étude présente une approche permettant d'identifier des fusions pathognomoniques de sarcome à partir de très faibles quantités de tissu fixé, de CTC sur des modèles murins ou chez des patients. La deuxième étude présentée s'intéresse à la détection de l'ADNct au diagnostic de rhabdomyosarcome en utilisant les altérations de nombre de copie de chromosome, les réarrangements chromosomiques et les variants de nucléotide. Nous avons démontré que la détection au diagnostic est faisable et a un impact pronostique fort sur le devenir des patients. La dernière partie de ce manuscrit présente le développement d'un processus de traitement d'échantillons de patient pour détecter et isoler des cellules tumorales circulantes dans le but d'analyser les particularités génomiques de cette population à une résolution cellulaire.Ce travail explore certains aspects de l'utilisation de la biopsie liquide dans les sarcomes pédiatriques, parmi de nombreux autres. Il est crucial dans le développement de ce champ de recherche, de maîtriser les particularités intrinsèques de chaque type tumoral et des technologies disponibles. Nous avons démontré l'utilité d'une telle approche au diagnostic dans deux applications. Cette aire de recherche ouvre de nombreuses possibilités qui appellent à poursuivre les efforts afin d'élargir les applications en recherche et en cliniqueAbstract: Liquid biopsy is an opportunity for improved diagnosis, treatment monitoring and genomic studies in oncology. Substantial effort in recent years has focused on circulating tumor DNA (ctDNA) and circulating tumor cells (CTC). However, pediatric cancer, including sarcomas, are still largely unexplored disease areas in this field.In this work, we sought to explore several aspects of liquid biopsy applied to pediatric sarcomas including their clinical use at diagnosis and as a tool to understand tumor biology. We first present a review of the literature demonstrating the feasibility of applying liquid biopsy to pediatric solid malignancies. Then, we report a methodological study using CTC for diagnostic purposes in translocation driven sarcomas. This approach identified fusions from as little as two unstained slides of FFPE tumor biopsy tissue, from CTC collected from tumor-bearing mice, and from liquid biopsy samples from patients with known fusion-positive cancers. The second study focuses on ctDNA for prognostication at the time of diagnosis in rhabdomyosarcoma by detecting copy number alterations, rearrangements, and single-nucleotide variants. Our study demonstrates that baseline ctDNA detection is feasible and has prognostic value. The last part of this work presents the development of a workflow to isolate single sarcoma cancer cells for sequencing, with an ultimate goal to analyze CTC genomic features at a single-cell resolution.This work explores several clinically and scientifically relevant aspects of liquid biopsy in pediatric sarcoma. We showed that liquid biopsy has utility at diagnosis in two different applications. Further development in this field will require a strong knowledge of tumor-specific biology, the clinical care of patients with these diseases, and the adaption of new technologies. My findings demonstrate the transformative possibilities this research may bring to the care of patients with pediatric sarcomas
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Tessmann, Jonathon. "Neuroendocrine genomics for tumor variant discovery." Thesis, University of Iowa, 2018. https://ir.uiowa.edu/etd/6305.
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An exome sequencing analysis pipeline was constructed to analyze NET germline and somatic samples. SNPs and INDELs were called and annotated from germline and somatic tissue. CNVs were also called for the tumor samples. This was accomplished using open source bioinformatics software that has been developed by the research community. Broad Institute "best practices" were followed. Some of the tools that were used include BWA, SAMtools, GATK, Varscan, VT, VEP, and GEMINI. Computational resources were provided by The University of Iowa NEON computer cluster. 57 germline samples and 15 tumor samples across 23 families with a history of NETs produced 4,452 germline variants, 1,695 somatic variants, 5,853 LOH events, and 627 CNV calls. False positive and driver candidacy filtering was applied. One family with Currarino syndrome has an inherited germline missense variant in MNX1. This variant has a phred-scaled Combined Annotation Dependant Depletion score of 35, putting it in the top 0.031% of deleterious variants. CNV analysis demonstrates that 8 of the 15 tumor samples have large-scale deletions of chromosome 18, three of which have nearly the entire chromosome deleted. An affected tumor suppressor gene in this region includes DCC, which is present in all three variant discovery techniques. Variant prioritization techniques are effective, but need further development to increase candidate variant/gene discovery rate.
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Jorge, Uana Maria Miguel. "Tumores gástricos primários múltiplos e únicos: análise imunohistoquímica comparativa." Universidade de São Paulo, 2006. http://www.teses.usp.br/teses/disponiveis/5/5154/tde-29012007-154954/.
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Introdução: Adenocarcinomas gástricos múltiplos primários (AGMP) são encontrados em 3,5% a 10% de todos os pacientes com câncer gástrico. A multiplicidade tumoral é amplamente reconhecida como indicador de predisposição genética para o desenvolvimento de neoplasias Além disso, as rotas de carcinogênese não estão claramente definidas nestes tumores (rota mutadora, ou supressora, ou da E-caderina). Objetivo: avaliar a imunoexpressão de hMLH1, hMSH2, e hMSH6 (rota mutadora), p53 (rota supressora) e E-caderina nos AGMP comparando-se com adenocarcinomas únicos (pareados quanto ao sexo, idade, tipo histológico, localização e estádio) e sua relação com dados clínico-patológicos. Casuística: dezenove pacientes com AGMP foram comparados a 21 pacientes com tumores gástricos únicos quanto a características imunohistoquímicas. Métodos: Blocos de tecido fixados em formalina a 10% e incluídos em parafina foram submetidos a cortes histológicos de 4 mm, para as avaliações histológica e imunohistoquímica para hMLH1, hMSH2, hMSH6, p53 e E-caderina. Resultados: A média de idade dos pacientes com AGPM foi de 66 + 9,06 anos, e de 60 + 16,9 anos nos pacientes com tumor único (P=0,56). Vinte e dois tumores estavam localizados na porção distal do estômago; 14, no corpo e cinco na porção proximal. Em 14 pacientes, as lesões eram próximas (< 3 cm), enquanto que, em cinco pacientes, as lesões estavam em outra porção do estômago. O estágio final anatomopatológico pós-operatório foi: 15 no estágio T1 (37,5%) (8 múltiplos e 7 únicos), 7 no estágio T2 (17,5%) (1 múltiplo e 6 únicos), 17 no estágio T3 (42,5%) (9 múltiplos e 8 únicos) e 1 no estágio T4 (27,5%) (1 múltiplo). Segundo a classificação de Laurén, 45 dos tumores foram do tipo intestinal (29 múltiplos e 16 únicos), 16 do tipo gástrico (12 múltiplos e 4 únicos) e um tumor do tipo misto (1 único). O estádio anatomopatológico revelou 30 tumores avançados (16 múltiplos e 14 únicos) e 32 precoces (25 múltiplos e 7 únicos). Na imunohistoquímica, não houve diferença entre a imunoexpressão nos dois grupos de tumores quanto a: hMLH1 (24,3% vs. 19% P=0,64), hMSH6 (4,8% vs. 2,4%, P=0,68), p53 (39% vs. 24%, P=0,35) e E-caderina (27% vs. 19%, P=0,46). hMSH2 foi positivo em todos os casos. Não houve associação entre os imuno-marcadores e os dados clínico-patológicos. Conclusões: 1. As rotas de carcinogênese, mutatora, supressora e E-caderina parecem estar independentemente envolvidas no desenvolvimento dos AGMP; 2. Não houve diferença de imunoexpressão dos marcadores analisados quando compararam-se os AGMP e os tumores únicos.Introduction: Multiple primary gastric adenocarcinomas (MPGA) have been reported from 3.5% to 10% of all patients with gastric cancer. Tumoral multiplicity is largely known as an indicator of genetic predisposition for the development of neoplasias. Moreover, the route of carcinogenesis has not been clearly clarified in these tumors (mutator pathway or suppressor pathway). Aim: to evaluate the immunoexpression of hMLH1, hMSH2, and hMSH6 (mutator pathway), p53 (suppressor pathway) and E-cadherin in the MPGA, comparing to solitary adenocarcinomas (similar gender, age, histological type, location and staging) and also the relation to the clinicopathological data.: Casuistics: Nineteen patients (Group 1) with MPGA were compared to 21 patients (Group 2) with solitary gastric tumors regarding clinicopathological characteristics and immunohistochemistry. Methods: Blocks of tissue fixed in 10% formalin and embedded in parafin were submitted to 4 mm sections for histological and immunohistochemistry analysis for hMLH1, hMSH2 and hMSH6 (mutator pathway), p53 (suppressor pathway) and E-cadherin. Results: The mean age for the MPGA was 66.8 + 9.06 years, and 59.0 + 16.9 years for the solitary tumor group(P = 0.27). Twenty-two tumors were in the distal stomach, 14 were in the body and five in the proximal portion. In 14 patients the lesions were close to each other (< 3 cm), while in five patients the neoplasias were distant, in another portion of the stomach.The final postoperative pathological stage was: T1 in 15 (eight multiple and seven solitary), T2 in seven (one multiple and six soliatry), T3 in 17 ( nine multiple and eight solitary) and T4 in one ( one multiple). According to the Laurén classification, 45 tumors were intestinal type (29 multiple and 16 solitary), 16 were diffuse (12 multiple and four solitart) and one mixed type ( one solitary). 30 tumors were diagnosed in advanced staging (16 multiple and 14 soliatry) and 32 were early (25 multiple and seven solitary). There was no difference between the hMLH1 immunoexpression in the two groups (24.3% vs. 19%, P=0.64), hMSH6 (4.8% vs. 2.4%, P=0.68), p53 (39% vs. 24%, P=0.35) and E-cadherin (27% v.s 19%, P=0.46). Immunostaining for hMSH2 was positive in all MPGA, indicating absence of alterations of this repair gene marker. There was no association between the immunomarkers and the clinicopathological data. Conclusions: 1. Routes of carcinogenesis, mutator, suppressor, and E-cadherin appear to be involved independently in the development of MPGA; 2. There was no difference in the markers immunoexpression in the two groups.
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Rabadán, Lozano M. Ángeles. "Genetic analysis of neural crest migration: Requirement of Dapper2-mediated inhibition of the Wnt canonical activity." Doctoral thesis, Universitat de Barcelona, 2012. http://hdl.handle.net/10803/83279.
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Numerous initiatives to improve our understanding of cancer biology have been lunched in different laboratories that aim to describe the interactome and gene-expression profile in different tumour cell line. It is now clear that the different strategies of cell migration observed in cancer are reminiscent of the different migratory strategies observed during embryo development. These similarities suggest that developmental program that has to be kept off after embryogenesis may be induced by spontaneous genetics modifications that produce tumour cells.
In this study we went inside the genetic network/profile that controls how neural crest cells eventually switch on the migration program and how they are able to arise into different lines with the propose of getting new ideas on how to prevent dissemination of tumour cells or how to treat advanced tumour that have already spread.
Neural progenitors of the dorsal neural tube that acquire the expression of specific neural crest determinants, delaminate from the neural tube and follow precise migratory pathways, to terminally differentiate into the various neural crest derivatives. Here we developed a novel resource for lineage trace and isolation of neural crest cells that allowed for a genome-wide expression screen in pre-migratory and migratory neural crest progenitors. We efficiently identified previously known neural crest specific genes. Expression profiling revealed new neural crest genes belonging to a wide range of cellular functions, with high representation of genes associated to cell motion. Additionally, we identified chick genes for which the human orthologues and/or paralogues are associated to Neuroblastoma formation.
In my thesis we identified new genes specifically expressed in the developing neural crest, and proposed a revised genomic signature for the normal neural crest cells. Furthermore, mutations on some of these genes are markers for Neuroblastoma tumour formation. Thus we propose this as a valid screen to identify candidates genes that contribute to the characterization of the Neuroblastoma cancer stem cells, and thus to the identification of specific targets to design new therapeutic strategies.
Getting in more detail into this genetic network, Wnt canonical signalling response has to been shown to be a key event in both cancer and neural crest cell development. Traditionally Wnt canonical pathway has been involved in neural crest induction process, but here we demonstrated that it is also critical for the onset migration of the neural crest cell. In fact, high levels of Wnt canonical activity prevents neural crest cell to delaminate and only through the inhibition of this activity mediate by dapper protein, neural crest cells can undergo into their normal migration pathways.
If this process has an implication in cancer is still unknown, but Dapper expression proteins have been already associated to different types of cancer.
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Ul-Hassan, Aliya Shabbir. "Genomic abnormalties in leiomyosarcoma and gastrointestinal stromal tumour." Thesis, University of Sheffield, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.489065.
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Leiomyosarcoma and GISTs are malignant tumours arising from the mesenchyme. Until relatively recently GISTs were classified as smooth muscle tumours such as leiomyosarcoma, however they are now recognised as a distinct entity arising from the interstitial cells of the Cajal.
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Centenaro, Vanessa Bridi. "Monossomia do cromossomo E3 em felinos FeLV positivos com neoplasias hematopoiéticas." Universidade Federal de Santa Maria, 2017. http://repositorio.ufsm.br/handle/1/13318.
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Hematopoietic tumors are the most common neoplastic disorders in felines. Many of these tumors are associated with infection by feline leukemia virus (FeLV) and one of the described mechanisms is the integration of viral material into the feline genome, which can lead to genomic instability and consequent alteration of genes related to proliferation control and cell death. When larger DNA fragments are affected, such changes can be observed by cytogenetic analysis. The present study aimed to observe cytogenetic changes in felines with hematopoietic neoplasms. The study was performed in eight felines, seven of them with a diagnosis of leukemia or lymphoma. The control consisted of a healthy feline FeLV negative with normal karyotype. At least 10 metaphases of each animal were analyzed. Additionally, 1000 lymphocytes of these two patients, were analyzed and classified cytologically by their viability (necrosis, apoptosis), mitotic state (mononuclear, binucleate (BN), mitotic multinucleate) and their chromosomal damage or instability state (presence of micronucleus (MN) in mononuclear, binucleate, as well as nuclear buds (NBUD). The results of this observation were statistically analyzed by the Wilcoxon paired test. In this chromosomal analysis two of these animals presented monosomy of the E3 chromosome, one with diagnosis of acute myeloid leukemia of the M6a (LMA-M6a) FAB subtype and another with multicenter lymphoma (LM). There were significant differences in LMA-M6a scores (N = 7, Z = 2.36, p = 0.01) and LM scores (N = 8, Z = 2.52, p = 0.01) when group control. However, there was no difference between AML and lymphoma (N = 8, Z = 0.07, p = 0.94). The E3 chromosome has 1401 genes, several related to cell cycle control (Plk1, Sun, Mad1l1, Mcm7), DNA repair (Pms2, Usp42), tumor suppression (Bcl7b). The loss of DNA fragments, such as the loss of the E3 chromosome in the two patients described, led to the haploinsufficiency of important genes for the cell cycle, and this could be a cause of genomic instability and consequently susceptibility to the development of cancer. The observation of cytogenetic alterations, in this way, allows a better understanding of the cancer in the feline species and translational research.Os tumores hematopoiéticos são os distúrbios neoplásicos mais comuns em felinos. Muitos desses tumores estão associados à infecção pelo vírus da leucemia felina (FeLV) e um dos mecanismos descritos é pela integração de material viral no genoma felino, que pode levar à instabilidade genômica e consequente alteração de genes relacionados com o controle da proliferação e morte celular. Quando fragmentos maiores de DNA são afetados, tais alterações podem ser observadas pela análise citogenética. O presente estudo objetivou observar as alterações citogenéticas em felinos com neoplasias hematopoiéticas. O estudo foi realizado em oito felinos, sete destes com diagnóstico de leucemia ou linfoma. O controle foi constituído por um felino saudável FeLV negativo com cariótipo normal. Foram analisadas no mínimo 10 metáfases de cada animal. Adicionalmente, destes dois pacientes foram analisados 1.000 linfócitos e classificados citologicamente pelo seu estado de viabilidade (necrose, apoptose), seu estado mitótico (mononucleado, binucleado (BN), multinucleado, mitótico) e seu dano cromossômico ou estado de instabilidade (presença de micronúcleo (MN) em célula mononucleada, binucleada, bem como brotos nucleares (NBUD). Os resultados dessa observação foram analisados estatisticamente pelo teste pareado de Wilcoxon. Nesta análise cromossômica dois destes animais apresentaram monossomia do cromossomo E3, um com diagnóstico de leucemia mieloide aguda do subtipo FAB M6a (LMA-M6a) e outro com linfoma multicêntrico (LM). Houve diferença significativa nas contagens de LMA-M6a (N=7; Z=2,36; p=0,01) e de LM (N=8; Z=2,52; p=0,01) quando comparados com o grupo controle. No entanto, não houve diferença entre LMA e linfoma (N=8; Z=0,07; p=0,94). No cromossomo E3 são descritos 1401 genes, sendo vários relacionados com controle de ciclo celular, (Plk1, Sun, Mad1l1, Mcm7), reparo de DNA (Pms2, Usp42) e supressão tumoral (Bcl7b).A perda de fragmentos de DNA, como o cromossomo E3 nos dois pacientes descritos, que leva a haploinsuficiência de genes importantes para o ciclo celular, poderia ser a causa de instabilidade genômica e, consequentemente suscetibilidade ao desenvolvimento do câncer. A observação de alterações citogenéticas, dessa forma, possibilita o melhor entendimento do câncer na espécie felina e serve como subsídio para a pesquisa translacional.
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Tomasini, Pascale. "Établissement d'un profil génomique spécifique des métastases cérébrales des adénocarcinomes bronchiques." Thesis, Aix-Marseille, 2019. http://www.theses.fr/2019AIXM0692.
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Le cancer bronchique est la première cause de mortalité par cancer, notamment parce qu’il est le plus grand pourvoyeur de métastases cérébrales (MC). Une meilleure connaissance de la biologie des cancers bronchiques non à petites cellules (CBNPC) a amélioré le pronostic des patients. Cependant, l’efficacité cérébrale des traitements est variable. Ce travail avait pour objectif une meilleure connaissance de la biologie des MC de CBNPC et de l’hétérogénéité génomique entre la MC et les autres sites tumoraux pour guider la prise en charge thérapeutique des malades.Nous avons montré que l’efficacité intracérébrale de l’immunothérapie était variable et que l’incidence et l’évolution des MC étaient associées au profil mutationnel. Nous avons ensuite comparé le séquençage pan-exomique de paires d’échantillons de tumeurs pulmonaires (TP) et MC de patients atteints de CBNPC et identifié 13 gènes spécifiques des MC.Nous avons ensuite constitué une cohorte prospective de patients atteints de CBNPC avec MC opérées. Dans ces MC, nous avons trouvé un nombre de mutations très élevé, dont 2 mutations des 13 gènes. De plus, l’ADNtc dans le LCR était représentatif des mutations des MC. Ces travaux soulignent l’importance de l’hétérogénéité tumorale entre les MC, les TP et l’ADNtc. Il est difficile d’établir une signature spécifique des MC, notamment du fait du faible nombre d’échantillons disponibles et de la difficulté d’obtenir des paires TP/MC mais l’étude de l’ADNtc dans le LCR peut être une piste. Nous allons ensuite étudier le microenvironnement cérébral et utiliser d’autres approches comme la modélisation mathématique pour une meilleure compréhension de la biologie des MCLung cancer is the leading cause of cancer-related deaths, partly because it is the first cause of brain metastases (BM). A better knowledge of non-small cell lung cancer (NSCLC) molecular biology and the development of targeted therapies have improved patients’ outcomes. However, the intracranial efficacy of these new treatments is inconstant. The objective of this work was a better knowledge of BM biology in lung adenocarcinoma and a better knowledge of genomic heterogeneity between BM and PT to guide patients’ treatment strategy.We showed that intracranial efficacy of immunotherapy was inconstant and that BM incidence and recurrence after local treatment was associated with mutation profile. We then compared whole exome sequencing of paired frozen samples from PT and BM of patients with NSCLC and identified 13 genes with recurrent mutations in BM never mutated in PT samples. We then analyzed a prospective cohort of patients with CBNPC and resected BM. In these BM, the number of mutations was high, including 2 genes among the 13 genes identified. Moreover, CSF ctDNA was representative of BM mutation status.This work highlights the importance of tumor heterogeneity between BM, PT and ctDNA. Whereas it is difficult to establish a specific signature of BM because of the poor number of samples available and the difficulty to have paired PT/BM samples for each patient, CSF ctDNA study may be a way to assess BM biology. We plan to study brain microenvironment and use new approaches such as mathematical modeling for a better understanding of BM biology
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Rooney, Patrick Hugh. "A genomic approach to the study of chemoresistance." Thesis, University of Aberdeen, 2000. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU602009.
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This study evaluated comparative genomic hybridisation (CGH) as a tool to detect candidate regions of the genome associated with chemoresistance. Using a variation on conventional CGH, DNA from three cell lines that were resistant to thymidylate synthase (TS) inhibitors (tomudex [TDX] or 5-fluorouracil [5-FU]) and their sensitive parent cells were evaluated. In MCF-7 and H630, cells that were resistant to TDX, a specific TS inhibitor with no other known cytotoxic potential, only a single region of change (18p gain) was apparent. The third cell line H630R10, which was resistant to 5-FU, had changes in several genomic regions following the acquisition of resistance, including 18p. Gain in the chromosomal region containing the TS gene (18pll.32) was detected by CGH in all three resistant cell lines. However, additional novel regions of interest were identified in the cells that were resistant to 5-FU, a cytotoxic agent known to have several other modes of cytotoxicity besides TS inhibition. These results suggested that CGH is of potential use in the detection of regions of the genome involved in chemoresistance. Having shown the potential of CGH as a tool for assessing chemoresistance at the genomic level, steps toward clinical application of this technique were evaluated. A prerequisite for study in archival pathology samples was successful DNA extraction and universal amplification of tumour DNA from paraffin-embedded tumour sections for CGH analysis. Degenerate oligonucleotide primed - polymerase chain reaction (DOP-PCR) was performed on minute quantities (50ngs) of fresh cell line DNA (H630R10) and tumour DNA (osteosarcoma), as well as paraffin-embedded DNA from the same case. The results of these DOP-PCR CGH reactions were compared with conventional CGH using l|0.g quantities of fresh DNA from both H630R10 cell line and osteosarcoma. The CGH profiles of the conventional CGH and DOP-PCR CGH did not show a high level of concordance, only 55% of the gains and 83.3% of losses detected by conventional CGH were detected by DOP-PCR CGH The use of universal amplification by DOP-PCR in paraffin-embedded sections was not taken forward into clinical evaluation. A study of colorectal cancer (CRC) was initiated which involved the microdissection of 29 Dukes' C CRC tumours from fresh frozen material for CGH analysis. This conventional CGH analysis of CRC tumours involved assessing each tumour twice by reversal of fluorochromes. Only genomic regions that were detected as changed in both forward and reverse profiles were accepted. This approach detected several regions of genome as changed across the 29 tumours. In all, 108 gains (a mean number of 3.7 aberrations per tumour, range 1-12) and 85 losses (a mean number of 2.9 aberrations per tumour, range 0-11) were detected in the 29 tumours. CGH analyses identified certain chromosomal regions as more likely to be changed than others. The most frequent aberrations detected across the 29 tumours was a loss of chromosomal arm 18q, seen in 31% of the tumours assessed. Gain was also common at some sites throughout the genome, for example, gain of chromosomal arms, 13q and 20q was seen in 27.6% of cases. Mann-Whitney U tests investigating the association between specific chromosomal aberrations such as gain of 20q or loss of 18q and known markers of CRC tumourigenesis (p53, p27, p21, Rb, cyclin Dl, PCNA, P-catenin, e-cadherin, c-erbB-2, bcl2, EGFR and c-erbB-2) assessed by immunohistochemistry (IHC) in 29 tumours found no association. Testing of the total number of genomic aberrations detected (loss + gain = genetic grade) rather than the frequency of aberration at specific chromosomal loci also found no association with the CRC tumour markers. Finally, the association between the chromosomal aberrations detected by CGH was investigated in relation to patient survival. This thesis has demonstrated the value of a global approach to the study of chemoresistance and tumourigenesis through the application of powerful technology such as CGH.
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Cyrta, Joanna. "A Pleiotropic Role of the SWI/SNF Complex in Cancer – Insights From Two Tumor Types : Small Cell Carcinoma of the Ovary, Hypercalcemic Type and Prostatic Carcinoma Role of Specialized Composition of SWI/SNF Complexes in Prostate Cancer Lineage Genomic Correlates of Clinical Outcome in Advanced Prostate Cancer." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASL045.
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Le complexe de remodelage de la chromatine SWI/SNF est un régulateur épigénétique majeur impliqué dans le développement embryonnaire et dans la différentiation cellulaire. De plus, les gènes qui encodent les sous-unités de SWI/SNF sont altérés dans au moins 20% de cancers. Bien que le complexe SWI/SNF soit le plus souvent considéré comme suppresseur des tumeurs, il existe des preuves croissantes que le rôle de SWI/SNF dans le cancer peut dépendre du type de tissu et du contexte.Dans la première partie de cette dissertation, nous présentons la caractérisation moléculaire d’une cohorte indépendante de carcinomes à petites cellules de l’ovaire de type hypercalcémiant (SCCOHT), comme exemple d’un cancer sous-tendu par des altérations perte-de-fonction de la sous unité catalytique de SWI/SNF, SMARCA4. Dans la deuxième partie, nous explorons le rôle du SWI/SNF dans le cancer de la prostate (CP), y compris ses formes les plus agressives : le CP résistant à la castration et le carcinome neuroendocrine. Alors que les mutations des gènes de SWI/SNF sont très rares dans le CP, nous montrons que l’expression de certaines sous-unités peut être dérégulée et qu’une haute expression de SMARCA4 est associée à des CP agressifs. De plus, nous montrons que plusieurs lignées cellulaires de CP dépendent de SWI/SNF pour leur croissance.Au total, ces deux exemples supportent l’hypothèse que SWI/SNF peut jouer des rôles différents dans le cancer en fonction du type tumoralThe SWI/SNF chromatin remodeling complex is a major epigenetic regulator involved in embryonic development and in cell differentiation. In addition, genes encoding components of SWI/SNF are altered in at least 20% of cancers. Even though the SWI/SNF complex is usually regarded as a tumor suppressor, there is increasing evidence that the role of SWI/SNF in cancer may be tissue type- and context-dependent.In the first part of this dissertation, we present the molecular characterization of an independent cohort of small cell carcinomas of the ovary, hypercalcemic type (SCCOHT), as an example of a malignancy driven by loss-of-function alterations of the catalytic subunit of SWI/SNF, SMARCA4. In the second part, we explore the role of SWI/SNF in prostate cancer (PCa), including its most aggressive forms: castration-resistant prostate cancer and neuroendocrine prostate cancer. We show that while SWI/SNF mutations are exceedingly rare in PCa, the expression of several SWI/SNF subunits can be deregulated and that high SMARCA4 expression is associated with aggressive PCa. In addition, we show that many PCa cell lines are dependent on SWI/SNF for their growth.Taken together, these two examples further support the hypothesis that SWI/SNF can play different roles in cancer, depending on the tumor type
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Rubio, Pérez Carlota 1990. "Understanding the genomic makeup of tumors to guide personalized medicine." Doctoral thesis, Universitat Pompeu Fabra, 2017. http://hdl.handle.net/10803/664287.
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Cancer is a disease of the genome. The study of tumor genomic alterations is used to guide several precision medicine strategies, some approved and a large number under clinical development. On the other hand, the study of tumor immunity is recently becoming the key for the success of other personalized strategies, named immunotherapies. Along this thesis I have made several contributions towards the advance of cancer precision medicine, based on the study of tumor “omics” data. First, I evinced the landscape of genomic-guided anti-cancer therapies. Second, I developed OncoPaD, a tool for the rational design of cost-effective cancer gene panels. Third, I contributed to the development of Cancer Genome Interpreter, a tool for the biological and therapeutic interpretation of variants found in newly sequenced tumors. Forth, I identified tumor intrinsic molecular mechanisms involved in tumor immune evasion.El càncer és una malaltia del genoma. L'estudi de les alteracions genòmiques dels tumors s’utilitza com a guia en varies estratègies de medicina de precisió, algunes d'elles aprovades i d'altres en assajos clínics. D'altra banda, l’estudi de la immunitat tumoral està esdevenint una peça clau per l’èxit d’altres estratègies terapèutiques, anomenades immunoteràpies. Al llarg d'aquesta tesi, mitjançant l'estudi de les dades “òmiques” tumorals, he contribuït de varies maneres cap a l'avenç de la medicina de precisió pel càncer. Primer, he identificat el panorama de les teràpies anticanceroses guiades per alteracions genòmiques. Segon, he desenvolupat OncoPaD, una eina pel disseny cost-efectiu i racional de panells de seqüenciació per càncer. A més, he contribuït al desenvolupament del Cancer Genome Interpreter, una eina que ajuda a la interpretació biològica i terapèutica de les variants presents a tumors novament seqüenciats. Per últim, he identificat diversos mecanismes mitjançant els quals els tumors són capaços d'evadir l’atac del sistema immunològic.
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Persson, Fredrik. "Studies of fusion oncogenes and genomic imbalances in human tumors /." Göteborg : Göteborg University, Lundberg Laboratory for Cancer Research, Dept. of Pathology, Sahlgrenska Academy at Göteborg University, 2007. http://hdl.handle.net/2077/7368.
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Low, Carolyn M. "Genomic interactions of the transcription factor VEZF1." Thesis, University of Glasgow, 2013. http://theses.gla.ac.uk/5078/.
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VEZF1 is a highly conserved vertebrate transcription factor. VEZF1 binding sites have been reported to function in gene promoter activation, insulator barrier activity and protection from de novo DNA methylation. This study aims to identify VEZF1 binding sites across the human genome and to develop a better understanding of the gene regulatory processes mediated by VEZF1.
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Michelland, Sylvie. "Déséquilibres génétiques dans les cancers bronchiques : une analyse par hybridation génomique comparative." Université Joseph Fourier (Grenoble), 1998. http://www.theses.fr/1998GRE10181.
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Le cancer du poumon est un probleme de sante publique majeur et il represente la premiere cause de mort par cancer chez l'homme dans le monde. Nous nous sommes interesses a l'analyse des desequilibres genetiques dans les tumeurs bronchiques dans le but d'etablir une cartographie precise des zones du genome associees a cette pathologie. Nous avons utilise la technique d'hybridation genomique comparative in situ (cgh) qui met en evidence de maniere rapide et globale l'ensemble des desequilibres genetiques presents dans une tumeur. Nous avons mis au point un protocole permettant d'obtenir des preparations de chromosomes metaphasiques adaptees a l'hybridation de type cgh et determine les conditions optimales requises pour une analyse cgh fiable et reproductible. Nous avons realise une etude cgh sur 11 tumeurs neuroendocrines de haut garde de malignite et 11 tumeurs non neuroendocrines. Nous avons montre que ces deux phenotypes partagent des anomalies communes et que certaines anomalies sont retrouvees specifiquement dans un phenotype. Ces resultats renforcent la notion qu'il existerait deux voies differentes de tumorgenese conduisant a la formation de ces deux classes de cancers bronchiques. Nous avons analyse un ensemble de 74 tumeurs bronchiques incluant tous les types histologiques. Notre but etant d'une part, d'identifier les regions chromosomiques specifiques pour chaque type histologique et d'autre part, d'etablir des correlations entre les anomalies chromosomiques mises en evidence par cgh, le type de cancer (ne, non ne), le type histologique et le degre de malignite de la tumeur. Les resultats ont montre des anomalies chromosomiques communes et differentes dans les differents types histologiques et nous avons etabli un patron d'anomalies chromosomiques pour chaque type histologique. Le nombre, le type et la distribution des anomalies permet de distinguer les carcinomes de haut grade et de bas grade de malignite. De plus, certaines anomalies semblent etre plus particulierement impliquees dans le caractere agressif des tumeurs. Ces resultats permettront ainsi d'orienter les recherches moleculaires visant a caracteriser les genes impliques dans le processus de cancerogenese.
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Usmani, Badar Alam. "Genomic instability and the metastatic potential of B16 murine melanomas." Thesis, University of Newcastle Upon Tyne, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.238763.
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Pages, Mélanie. "Integrative genomic, epigenetic, radiologic and histological characterization of pediatric glioneuronal tumors." Thesis, Sorbonne Paris Cité, 2018. http://www.theses.fr/2018USPCB217.
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Pas de résuméThe large-scale genomic studies performed recently has enabled the objective identification of numerous novel genomic alterations and highlighted that pediatric brain tumors often harbor quiet cancer genomes, with a single driver genomic alteration. This characteristic is of special interest in the current context of precision medicine development. Low-grade glioneuronal tumor group is highly heterogeneous and remains particularly challenging since it includes a broad spectrum of tumors, often poorly discriminated by their histopathological features and not completely molecularly characterized. We used targeted methods (IHC, FISH, targeted sequencing), and large scale genomic and epigenetic methodologies to perform an integrative analysis to further characterized papillary glioneuronal tumors (PGNT), midline gangliogliomas and dysembryoplastic neuroepithelial tumors (DNT). We demonstrated that PGNT is a distinct entity characterized by a PRKCA fusion. We highlighted that H3 K27M mutation can occur in association with BRAF V600E mutation in midline grade I glioneuronal tumors, showing that despite the presence of H3 K27M mutations, these cases should not be graded and treated as grade IV tumors because they have a better spontaneous outcome than classic diffuse midline H3 K27M-mutant glioma. The DNT study enable us 1) to specify that non-specific DNT corresponds to a clinico-histological tumor group encompassing diverse molecularly distinct entities and 2) to demonstrate that specific DNTs can be progressive tumors and harbored a distinct DNA methylation profile. Diagnosis and genomic profiling that can guide precision medicine require tissue acquisition by neurosurgical procedures that are often difficult or not possible. We validated a sample collection procedure and we developed methodologies to detect circulating tumor DNA (ctDNA) in CSF, plasma and urine to identify clinically relevant genomic alterations from a cohort of 235 pediatric patients with brain tumors. We optimized a method to process ctDNA and performed ultra-low pass whole genome sequencing (ULP-WGS) using unique molecular identifiers, confirming we can reliably construct sequencing libraries from CSF-, plasma- and urine-derived ctDNA. ULP-WGS has also been used to assess sequencing library quality, copy number variations (CNVs) and tumor fraction. The vast majority of samples undergoing ULPWGS exhibited no CNVs, consistent with either absence in the tumor or low levels of tumorderived cfDNA. To distinguish between these, we developed a hybrid capture sequencing panel allowing identification of specific mutations and fusions more common in pediatric brain tumors
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Marjanovic, Nemanja. "Application of the single cell genomics in deciphering tumor heterogeneity and its role in tumor progression and drug resistance." Thesis, Massachusetts Institute of Technology, 2021. https://hdl.handle.net/1721.1/130830.
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Thesis: Ph. D., Massachusetts Institute of Technology, Computational and Systems Biology Program, February, 2021Cataloged from the official PDF of thesis. "February 2021."
Includes bibliographical references.
Tumor progression, from the single mutated cell to the advanced stages of cancer, represents an evolutionary process. During tumor progression, cancer cells acquire new genetic mutations, becoming more heterogeneous, leading to tumor progression and resistance to therapy. However, clear genetic drivers of progression, metastasis, and therapeutic resistance are identified in only a subset of tumors, pointing to non-genetic contributors to cancer progression. Also, somatic evolution in cancer is occurring at the level of the single cell. Therefore, the application of the single cell genomic method is crucial for deciphering phenotypic heterogeneity. Here, we profiled single cell transcriptomes from genetically engineered mouse lung tumors at seven stages spanning tumor progression from atypical adenomatous hyperplasia to lung adenocarcinoma. The diversity of transcriptional states spanned by tumor cells increased over time and was reproducible across tumors and mice, but was not explained by genomic copy number variation. Cancer cells progressively adopted alternate lineage identities, computationally predicted to be mediated through a common transitional, high-plasticity cell state (HPCS). HPCS cells prospectively isolated from mouse tumors had robust potential for phenotypic switching and tumor formation and were more chemoresistant in mice. Our study reveals transitions that connect cell states across tumor evolution and motivates therapeutic targeting of the HPCS.
by Nemanja Marjanovic.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Computational and Systems Biology Program
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Ng, Kiu Yan Charlotte. "Tumour evolution in ovarian cancer using high-throughput genomics technologies." Thesis, University of Cambridge, 2012. https://www.repository.cam.ac.uk/handle/1810/265590.
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High-grade serous ovarian carcinoma (HGSOC) is characterised by genomic instability, ubiquitous TP53 loss, widespread disease at diagnosis and the frequent emergence of platinum resistance. This thesis explores the use of high-throughput genomics technologies to understand if resistance could be explained by the model of tumour evolution. We performed SNP array analysis of a cell line model system of platinum resistance consisting of matched cell lines from three cases of HGSOC established before and after clinical resistance developed, the OVOl clinical study consisting of six matched pairs of tumours before and after three cycles of chemotherapy, and the OV03/0V04 study consisting of 18 cases sampled at multiple timepoints and from multiple metastatic sites. The results showed evidence of metastatic site dependent divergence. Moreover, mutually exclusive loss of heterozygosity patterns between presentation and relapse genomes, including all the cases in the cell line system and one of two OV03 cases for which relapse material was available, suggest that the relapse arises from a minor subclone of the presentation disease, while in the remaining case, the subclone with an NFJ homozygous deletion was enriched in the relapsed disease. I then asked which mutational process drives evolution. Using next-generation sequencing (NGS), I compared the structural variants between and within cases in the model system and in 6 cases of the OV03 cohort. From the genomic signatures in the cell lines, I demonstrated that a case with homologous recombination (HR) deficiency acquired numerous translocations and small deletions (median size of 13.4kb) , whereas another showed a novel tandem duplicator phenotype (median size of tandem duplications was 350kb). Mutator phenotypes in both cases arose early in progression and persisted, but the tumour with HR deficiency showed evidence of re-stabilising its ,"genome and lost platinum sensitivity after a revertant BRCA2 mutation restored its HR function. A subset of tumours from the Cancer Genome Atlas (TCGA) dataset suggested that these two phenotypes were mutually exclusive. Amongst the six OV03 cases, preliminary analysis suggests that one case showed an amplifier phenotype and three cases showed evidence of parallel evolution. Taken together, early onset of mutator phenotypes and parallel evolution may provide a mechanism by which resistance evolves. Further work should aim to identify the processes involved in tumour evolution in 'purified' populations such as cancer stem cells.
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Turón, Rodrigo Gemma. "A genome editing based approach to study tumor cell heterogeneity." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/667524.
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Colorectal tumors are not homogeneous entities but rather composed of a mixture of cells with different phenotypes, reminiscent of healthy intestinal epithelium cell types. Intestinal epithelium is one of the organs with highest self-renewal rate, maintained by a pool of highly proliferating stem cells located at the base of the crypts. Daughters of the stem cells abandon the crypts and differentiate as they move up the villi, in a process that takes no longer than six days. Recent findings suggest that colorectal cancers (CRCs), like normal intestine, rely on a stem cell hierarchy for its growth. Cancer stem cells, identified by LGR5 gene expression, are at the apex of this hierarchy, and are thought to be the drivers of CRC expansion and metastasis. This thesis is focused on characterizing the growth dynamics of the different tumor compartments and identifying the cells that fuel tumor growth. Moreover, we have also tried to elucidate which is the cell of origin of metastasis.
To complete this project we have first developed new models to study human disease, as most of the previous work relied on genetically modified mouse models to reproduce the disease. Here, we have combined patient-derived organoid 3D cultures and CRISPR/Cas9 genome editing techniques to insert fluorescent reporter proteins under the control of our genes of interest. This has allowed us to visualize different tumor cell types in vivo using LGR5, KRT20 and EMP1 as markers for stemness, differentiation and invasion respectively. In addition, we have also set up a system to follow the progeny of the abovementioned populations in vivo in intact tumors.
We have identified the different tumor compartments by subcutaneously injecting modified human organoids into immunosuppressed mice. Flow cytometry purification and reinjection into secondary hosts of stem-like and differentiated-like cells has enabled us to discover that cancer cells retaining stem cell characteristics are more proficient in tumor initiation than the rest of the tumor. Nevertheless, lineage tracing of the abovementioned genes in an intact tumor cell environment shows how both stem and differentiated progenies are able to give rise to long lasting clones and thus equally fuel tumor growth. Furthermore, we have observed plasticity arising from both cell types, indicative that the cellular hierarchy is disrupted during tumor progression.
In addition, we have defined EMP1 as a putative gene marker for invasive cells. EMP1-High cells are a differentiated subset of tumor cells that harbor migratory properties and secrete myeloid recruiting chemokines to the tumor site. Myeloid cells have been shown to contribute to all steps of metastasis in several cancer types. We hypothesize that this EMP1+ subpopulation is the one that disseminates from the primary tumor and initiates metastasis. For metastatic studies, we have resorted to mouse derived tumor organoids that allow the growth of primary and metastatic disease in fully immunocompetent ice, and we have set up new models to study disease relapse in metastatic sites upon primary tumor removal
Taken together, our data provides new insights on the mode of tumor growth in advanced human colorectal carcinomas and suggests that stem cell traits are not required for tumor growth neither metastatic spread, contrary to what was initially though based on mouse adenoma studies.Els tumors colorectals no són una entitat homogènia sinó que estan formats per una barreja de cèl·lules de fenotips variats, reminiscents dels tipus cel·lulars de l’epiteli intestinal sa. Estudis recents suggereixen que el creixement del càncer colorectal (CCR), igual que el de l’intestí normal, està mediat per una jerarquia amb origen en cèl·lules mare. Les cèl·lules mare del càncer, identificades per l’expressió del gen LGR5, es troben a l’àpex de la jerarquia i impulsen l’expansió del CCR i la metàstasis. Aquesta tesi se centra en caracteritzar la dinàmica d’expansió dels diferents compartiments tumorals i en identificar les cèl·lules que en mantenen el creixement. També hem intentat elucidar quina és la cèl·lula d’origen de la metàstasi. Per a realitzar aquest projecte primer hem desenvolupat nous models per estudiar la malaltia humana, combinant el cultiu d’organoids derivats de pacients i l’edició genòmica mitjançant CRISPR/Cas9. Això ens ha permès visualitzar diferents tipus cel·lulars tumorals in vivo usant LGR5, KRT20 i EMP1 com a marcadors de cèl·lula mare, cèl·lula diferenciada i cèl·lula invasiva, respectivament. Addicionalment, també hem establert un sistema per seguir la progènie de les poblacions mencionades. Hem descobert que tant el compartiment de cèl·lules mare com el diferenciat són capaços de donar lloc a una progènie que persisteix en el temps, suggerint que ambdós tipus cel·lulars contribueixen al creixement tumoral. A més a més, hem observat plasticitat entre els dos compartiments, cosa que indica que la jerarquia cel·lular es perd durant el desenvolupament del tumor. Finalment, mitjançant l’ús d’EMP1 com a marcador de cèl·lules invasives hem identificat un subgrup de cèl·lules diferenciades amb propietats migratòries i amb potencial per reclutar cèl·lules mieloides. La nostra hipòtesi és que la població EMP1+ és la que dissemina del tumor primari i inicia la metàstasi. En resum , les nostres dades suposen una nova visió en l’estudi del mode de creixement del càncer de colon d’estadis avançats en humà, i suggereixen que els trets de cèl·lula mare no són necessaris per creixement tumoral ni la disseminació metastàtica, contràriament al que es pensava inicialment, degut als estudis realitzats en adenoma de ratolí.
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Núñez, Ollé Marc 1984. "The Role of cyclin O in the DNA damage response." Doctoral thesis, Universitat Pompeu Fabra, 2014. http://hdl.handle.net/10803/459302.
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Cyclin O, a novel identified CDK1 and CDK2-binding cyclin, has been demonstrated to be required for γ-radiation induced apoptosis in a lymphoid cell line. Ɣ-radiation induces the formation of DSBs in the DNA what activate the DDR in order to mitigate the consequences of this insult and repair the DNA damage. The aim of this thesis has been to study the role of Cyclin O in activation of the DDR in response to γ-radiation and the consequences in the cell survival. Using Cyclin O deficient cells as a cellular model, we have found that the Cyclin O limits the DNA resection, a process that drives the cell to repair the DNA damage by HR. Moreover, we have seen that ATM activation and some of its downstream targets are not properly activated after DNA damage in Cyclin O deficient cells. We also have found that Cyclin O complexes are able to phosphorylate ATM in vitro opening the door to study a new mechanism of the DDR regulation by Cyclin O.La Ciclina O és una nova ciclina que interacciona amb CDK1 i CDK2, i que s’ha demonstrat ser necessària per l’apoptòsi induïda per radiació gamma en una linia cel·lular d’origen linfoide. La radiació gamma indueix la formació de talls de doble cadena (DSBs) al DNA activant la resposta per dany al DNA (DDR) per tal de reduïr-ne les conseqüències citotòxiques i reparar el dany al DNA. L’objectiu d’aquesta tesi ha esta el d’estudiar el paper de la Ciclina O en l’activació de la resposta per dany al DNA i les conseqüències sobre la supervivència cel·lular. Utilitzant cèl·lules deficients en Ciclina O com a model, hem trobat que la Cyclina O limita el processament dels talls de doble cadena necessaris per a la reparació del dany al DNA per recombinació homologa. També hem una deficient activació d’ATM i la fosforil·lació d’alguns substrats d’aquesta proteína en cèl·lules deficients per la Ciclina O. Finalment, hem vist que els complexes de Ciclina O fosforil·len ATM in vitro, un fet que obre una porta a l’estudi de nous mecanismes de regulació de la resposta per dany al DNA mitjançant la Ciclina O.
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Leung, Tsin-wah. "Imprinting genes in gestational trophoblastic diseases /." View the Table of Contents & Abstract, 2006. http://sunzi.lib.hku.hk/hkuto/record/B36434504.
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Leung, Tsin-wah, and 梁展華. "Imprinting genes in gestational trophoblastic diseases." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2006. http://hub.hku.hk/bib/B45010845.
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Fong, Jim Chi Wai. "The role of PTTG and PBF in genomic instability and DNA repair in thyroid cancer." Thesis, University of Birmingham, 2016. http://etheses.bham.ac.uk//id/eprint/6902/.
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Thyroid cancer, the most common endocrine malignancy has a rising incidence worldwide. Radiation damage is a known aetiological factor in thyroid tumourigenesis, particularly in children. Pituitary tumor transforming gene (PTTG) and its binding partner (PTTG binding factor; PBF) are overexpressed in thyroid cancers. Critically, PTTG and PBF have been shown to be independent markers of poor prognosis in thyroid cancer. PTTG, a human securin, has multifunctional roles in mitotic control, DNA repair, apoptosis, cell transformation and genomic instability. PBF, which has independent tumourigenic and transforming actions, binds to PTTG, transports it to the nucleus and facilitates its actions within the nucleus. Taken together, the above implicate the functional role of PTTG and PBF in genetic instability. This thesis describes the generation of a transgenic murine model of thyroid cancer which overexpressed both human PTTG and human PBF in the thyroid gland (BI-Trans). The BI-Trans murine model developed goitres from a young age in both genders. Additionally, they develop thyroid adenomas at a later age which had a female preponderance. Unexpectedly, this BI-Trans murine model did not develop cancers. We next measured the index of genetic instability (GI) in the thyroids of our transgenic murine models with fluorescent inter-simple sequence repeat-PCR (FISSR-PCR). This technique was refined to measure GI with small quantities of DNA obtained from murine thyroids. We performed microarray analysis on our murine thyroids with and without ionising radiation to elucidate the mechanism by which PBF and PTTG induced genetic instability.
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Kiebish, Michael Andrew. "Mitochondrial lipidome and genome alterations in mouse brain and experimental brain tumors." Thesis, Boston College, 2008. http://hdl.handle.net/2345/27.
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Thesis advisor: Thomas N. SeyfriedMitochondria are the key regulators of the bioenergetic state of the cell. Damage to mitochondrial protein, DNA, or membrane lipids can result as the cause or affect of disease pathology. Regardless, this damage can impair mitochondrial function resulting in a decreased ability to produce ATP to support cellular viability. This thesis research examined the mitochondrial lipidome by shotgun lipidomics in different populations of C57BL/6J (B6) brain mitochondria (non-synaptic and synaptic) and correlated lipid changes to differences in electron transport chain (ETC) activities. Furthermore, a comparison was made for non-synaptic mitochondria between the B6 and the VM mouse strain. The VM strain has a 1.5% incidence of spontaneous brain tumors, which is 210 fold greater than the B6 strain. I determined that differences in the brain mitochondrial lipidome existed in the VM strain compared to the B6 strain, likely corresponding to an increased rate of spontaneous brain tumor formation. Analysis of the mitochondrial genome in the CT-2A, EPEN, VM-NM1, and VM-M3 brain tumors compared to their syngeneic controls mouse strains, C57BL/6J (B6) and VM mice, was examined to determine if mutations existed in experimental brain cancer models. No pathogenic mtDNA mutations were discovered that would likely cause a decrease in the mitochondrial functionality. A novel hypothesis was devised to examine the tumor mitochondrial lipidome to determine if quantitative or molecular species differences existed that could potentially alter the functionality of the ETC. Brain tumor mitochondria were examined from tumors grown in vivo as well as in vitro. Numerous lipid differences were found in the mitochondria of brain tumors, of which the most interesting involved the unique molecular speciation of cardiolipin. ETC activities were significantly decreased in the primary ETC complexes which contribute protons to the gradient as well as the linked complexes of brain tumor mitochondria compared to controls. Taken together, it is likely that differences in the mitochondrial lipidome of brain tumors results in severe impairment of the mitochondria’s ability to produce ATP through the ETC. This research has provided a new understanding of the role of mitochondrial lipids in brain as well as brain cancer and offers an alternative explanation for metabolic dysfunction in cancer
Thesis (PhD) — Boston College, 2008
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
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De, Mattos Arruda Leticia. "Genomic characterisation of brain malignancies through liquid biopsies: The cerebrospinal fluid-derived circulating tumour DNA better represents the genomic alterations of brain tumours than plasma." Doctoral thesis, Universitat Autònoma de Barcelona, 2016. http://hdl.handle.net/10803/394019.
Full textAbstract:
Los recientes avances en la secuenciación masiva en paralelo y en las técnicas genómicas digitales apoyan la validez clínica del ADN libre tumoral circulante (ctDNA) como una "biopsia líquida” en el cáncer humano. La presencia de ctDNA en el plasma puede ser útil para identificar alteraciones genómicas, monitorizar la respuesta al tratamiento, identificar la resistencia terapéutica, y potencialmente caracterizar la heterogeneidad del tumor.
El estudio de prueba de concepto en el campo de las biopsias líquidas titulado “Capturing intra-tumor genetic heterogeneity by de novo mutation profiling of circulating cell-free tumor DNA: a proof-of-principle” publicado en la revista Annals of Oncology en julio de 2014, es el artículo complementario analizado en esta tesis. Este artículo es uno de los primeros en demostrar que la secuenciación masiva en paralelo del ctDNA derivado del plasma constituye una herramienta potencial para la identificación y el seguimiento de las alteraciones genómicas somáticas durante el curso de la terapia dirigida, y que esta herramienta no invasiva se puede emplear para superar los retos planteados por la heterogeneidad del tumor.
El ctDNA derivado del plasma ha demostrado ser capaz de identificar las alteraciones genómicas de los pacientes con cáncer. Sin embargo, los pacientes con tumores cerebrales tienen cantidades bajas o indetectables de ctDNA en el plasma lo que excluye la caracterización genómica del cáncer de cerebro a través del ctDNA en el plasma. La prueba de concepto en el campo de las biopsias líquidas del sistema nervioso central, que es el artículo fundamental analizado en este tesis: “Cerebrospinal fluid-derived circulating tumour DNA better represents the genomic alterations of brain tumours than plasma”, fue publicado en Nature Communications en noviembre de 2015. El ctDNA derivado de tumores malignos del sistema nervioso central primario y secundario esta enriquecido en el líquido cefalorraquídeo (LCR) y retrata las alteraciones genómicas de las enfermedades del sistema nervioso central mejor que el plasma. Los niveles de CSF ctDNA fluctúan longitudinalmente en el tiempo y siguen los cambios en la carga tumoral cerebral, proporcionando biomarcadores para monitorizar los canceres cerebrales. Además, el LCR ctDNA ha demostrado facilitar y complementar el diagnóstico del carcinomatosis leptomeníngea.
El ctDNA presente en el LCR de neoplasias cerebrales y el ctDNA presente en el plasma de los cánceres de mama con metástasis sistémicas extra-craneales podría ser utilizado para caracterizar las alteraciones genómicas de las metastasis de estos cánceres. El uso de los CSF ctDNA representa una herramienta mínimamente invasiva que puede cambiar el paradigma para el manejo clínico de los pacientes con tumores malignos en el sistema nervioso central. Las biopsias líquidas tienen el potencial de proporcionar la información genómica completa del tumor, secuencial y en tiempo real y que permitirá mejorar el manejo terapéutico de los pacientes con cáncer.Recent developments in massively parallel sequencing and digital genomic techniques support the clinical validity of cell-free circulating tumour DNA (ctDNA) as a ‘liquid biopsy’ in human cancer. ctDNA in plasma may be useful to identify actionable genomic alterations, monitor treatment responses, unravel therapeutic resistance, and potentially to characterise tumour heterogeneity. The proof-of-principle study in the field of liquid biopsies, which is the ancillary article analysed in this thesis entitled: “Capturing intra-tumor genetic heterogeneity by de novo mutation profiling of circulating cell-free tumor DNA: a proof-of-principle” was published in Annals of Oncology in July 2014. This article is one of the first to demonstrate that high-depth targeted massively parallel sequencing of plasma-derived ctDNA constitutes a potential tool for de novo mutation identification and monitoring of somatic genomic alterations during the course of targeted therapy. This article demonstrated that plasma ctDNA may be employed to overcome the challenges posed by tumour heterogeneity. Plasma-derived ctDNA has been shown to be informative of the genomic alterations of patients with cancers. Nevertheless, patients with brain tumours have low or undetectable amounts of ctDNA in plasma precluding the genomic characterisation of brain cancer through plasma ctDNA. The proof-of-principle in the field of central nervous system liquid biopsies, which the fundamental article analysed in this thesis entitled: “Cerebrospinal fluid-derived circulating tumour DNA better represents the genomic alterations of brain tumours than plasma” was published in Nature Communications in November 2015. ctDNA derived from primary and secondary central nervous system malignancies was shown to be more abundantly present in the cerebrospinal fluid (CSF) than in plasma and it portrayed the genomic alterations of central nervous system disease better than plasma. CSF ctDNA levels longitudinally fluctuated in time and followed the changes in brain tumour burden providing biomarkers to monitor brain malignancies. Additionally, CSF ctDNA was shown to facilitate and complement the diagnosis of leptomeningeal carcinomatosis. Taken together, ctDNA present in the CSF of brain malignancies and ctDNA present in the plasma of breast cancers with extra-cranial systemic metastases may be used to characterise metastasis-specific genomic alterations. CSF ctDNA represents a minimally invasive tool that may change the paradigm for the clinical management of cancer patients with central nervous system malignancies. Liquid biopsies have the potential to provide comprehensive, sequential and real-time tumour-derived genomic information that will improve the therapeutic management of cancer patients.
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Strakova, Andrea. "Genome diversity and evolution in canine transmissible venereal tumour." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/276037.
Full textAbstract:
The canine transmissible venereal tumour (CTVT) is a contagious cancer that is naturally transmitted between dogs by the allogeneic transfer of living cancer cells during coitus. CTVT first arose several thousand years ago and has been reported in dog populations worldwide. The goals of this Thesis were (1) to gain further understanding of CTVT distribution patterns and prevalence around the world, (2) to use genetics to trace the historical spread of CTVT and (3) to map the genetic as well as phenotypic diversity of CTVT tumours around the world. To understand the distribution patterns of CTVT, I obtained information from 645 veterinarians and animal health workers in 109 countries, and generated a snapshot of the locations in which this disease is found. Additionally, as preparation for further genetic analysis, I collected samples from over one thousand CTVT cases from more than 50 countries, optimised methods for high-throughput DNA extraction and quantification and optimised a qPCR-based assay for CTVT diagnosis and host contamination detection. With the goal of tracing the historical spread of CTVT and learning about the genetic diversity of this disease, I sequenced complete mitochondrial genomes of 449 CTVT tumours and their matched hosts. The analysis of the CTVT mitochondrial diversity revealed that CTVT has captured mitochondrial DNA (mtDNA) through horizontal transfer events at least five times during the history of the lineage, delineating five tumour clades. CTVT appears to have spread rapidly around the world within the last 2,000 years, perhaps transported by dogs travelling along historic maritime trade routes. This work indicated that negative selection has operated to prevent accumulation of deleterious mutations in captured mtDNA, and that recombination has caused occasional mtDNA re-assortment. A histology-based screen of CTVT clades did not show any significant phenotypic differences between groups. In order to determine how the five mtDNA clades relate to each other, I analysed data from 539 CTVT exomes. This revealed that a single canine mtDNA haplogroup has recurrently and recently undergone multiple horizontal transfer events. Analysis of this haplotype highlighted a number of candidate genetic variants which may be conferring a selective advantage to this haplotype in CTVT, possibly by influencing mtDNA transcription or replication. Overall, genetic and phenotypic analysis of CTVT tumours from across the globe has broadened our understanding of CTVT diversity, and provided important insights into the biology of a unique transmissible cancer.