Le carcinome hépatocellulaire (CHC) est la forme la plus fréquente de cancer du foie et l’une des principales causes de mortalité par cancer dans le monde. Il s’agit d’une maladie de mauvais pronostic, aux ressources thérapeutiques limitées, hétérogène sur le plan immunophénotypique et génomique, qui se développe très souvent sur un foie remanié cirrhotique. Les études moléculaires ont révélé plusieurs sous-classes de CHC caractérisés par des signatures génomiques et protéomiques distinctes. Au cours de mon travail de thèse, nous avons contribué à améliorer notre compréhension de la biologie des CHC et des classifications moléculaires en cartographiant le génome non-codant de tumeurs de CHC induites par des virus hépatotropes (VHB, VHC) et en étudiant la sous-classe moléculaire de CHC la plus agressive KRT19-positif. Nous avons établi la première carte de transcriptome à ARN non codants du CHC et révélé une forte activation intra-tumorale des rétrotransposons à LTR, qui sont principalement inhibés dans les cellules hépatiques normales, dans des CHC induits par les VHB et VHC. Certains des transcrits dérivés de LTR se sont révélés être des régulateurs clés de l’expression génique et donc activer la croissance cellulaire. Dans la deuxième étude, nous identifions une nouvelle voie de régulation des CHC KRT19-positif affectant le métabolisme énergétique de ces tumeurs. Les CHC KRT19-positif sont des tumeurs fortement glycolytiques liée à une activation de la réponse à l’hypoxie. L’excès de production par les CHC KRT19-positif de l’oncométabolite 2-hydroxyglutarate en absence de mutation des gènes IDH1 et IDH2 était associé à un profil aberrant hyperméthylé sur la lysine 9 de l’histone H3 (H3K9me3) suggérant une répression de la transcription notamment des gènes impliqués dans la différenciation cellulaire. / Hepatocellular carcinoma (HCC) is the main primary liver cancer and one of the most leading cause of cancer-related death worldwide. This heterogeneous disease with a worse prognosis has been subjected of numerous studies aimed to establish global phenotypic profiles. During my thesis, I dedicated my work to improve these classifications by identifying signatures on the non-coding genome and working on a very aggressive form of HCC expressing progenitors markers. With help of a Japanese team, we demonstrated that LTR-derived ncRNAs were active in HCC and that correlation correlates with expression of common cancer markers (GPC3) ans TP53 mutations. This signature can also be used to discriminate HCCs at high risk of recurrence. Finally, we have showed that these LTRs are detectable on prenoplastic stages in the Mdr2 KO mouse model. In parallel, I worked on HCC that expresses progenitor markers such as cytokeratin 19. Using proteomic and transcriptionnal approaches and in silico analyses, we propose that the occurrence of this type of cancer id due to an hypoxic event likely related to trans-arterial chemoembolization. These tumors have a highly glycolytic phenotype with production of an oncometabolite (2-hydroxyglutarate) that has been generally foubd in IDH1/2 mutated cholangiocarcinomas. Finally we suggest the use of metformin, type 2 diabetes drug, to reverse metabolic reprogramming and restore sensitivity to chemotherapy

<p>The human skin provides us with an excellent protective barrier and possesses a remarkable ability of constant renewal. Basal cell carcinoma is the most common type of skin cancer. The aim of this project was to verify results from an earlier study investigating the molecular differences between basal cell carcinoma (BCC) and basal cells of normal human epidermis. In that study microdissection of cell populations from BCC and basal cells of normal epidermis respectively was performed in five cases of confirmed BCC. Following RNA extraction and amplification, a gene expression analysis was performed using a 46 k human cDNA microarray. Comparison of expression profiles showed a differential expression of approximately 300 genes in BCC. An upregulation of signaling pathways previously known to be of importance in BCC development could be observed, as well as a downregulation of differentiation markers, MHC class II molecules, and proteins active in scavenging of oxygen radicals. We wanted to confirm these findings for a number of selected genes, using real time PCR. The focal point of this project was microdissection of cells from BCC and subsequent isolation of RNA. Microdissection based methods offer a possibility of selecting well defined cell populations for further analysis by using a focused laser beam. Initially tests in order to optimize the method were also performed, concerning the dehydration process and choice of slides used in microdissection. Isolation of RNA may, as we experienced, be associated with problems due to destruction of RNA by degrading enzymes.</p>

Diss. (sammanfattning) Umeå : Umeå universitet, 2005. / Härtill 4 uppsatser.

Thesis (Ph. D. in Chemistry)--Vanderbilt University, May 2005. / Title from title screen. Includes bibliographical references.

FSGS (focal segmental glomerulosclerosis) is a pathologic pattern that affects the glomerulus of the kidneys and is associated with progression toward end-stage kidney disease. It is characterized by destruction of the glomerular filtration system and replacement by scar tissue, which leads to chronic renal failure. An increase in glomerular capillary pressure may be an important factor in glomerulosclerosis. The podocyte is a major structural component of the filtration barrier. Since podocytes have an important role in maintaining the structural and functional integrity of glomerular filtration, a chronic increase in glomerular filtration pressure could ultimately damage and compromise the podocyte filtration apparatus. The segmental nature of FSGS suggests that podocyte damage may only occur at specific regions in the glomerulus. This poses the question as to whether differences in podocyte function, assessed by gene expression, may be dependent on their location in the glomerulus, and these regional differences might be responsible for FSGS development. Consequently, in order to evaluate this hypothesis there is a need to selectively isolate podocytes from various regions in a glomerulus. Therefore, the objective of this study was to determine the feasibility of selectively isolating podocyte cells from other renal cells using laser capture microdissection (LCM), and analyzing gene expression in these isolated cells using quantitative real-time polymerase chain reaction (qRT-PCR). If feasible, this method could be used to examine isolated cells for unique podocyte gene expression patterns that vary regionally throughout the glomerulus, and identify potential molecular and cellular mechanisms responsible for the initiation and progression of FSGS. Such information could then be used to identify new and pharmacologically accessible molecular targets. The specific goals of this project were to: 1) determine the feasibility of employment of the LCM system in the Boston University Department of Pathology for the capture of isolated mouse podocytes. 2) determine optimal tissue preservation and preparation methods for laser capture and mRNA analysis of isolated podocytes; and 3) determine the minimum number of isolated podocytes required to analyze gene expression using qRT-PCR. The results show that 1) liquid nitrogen was the preferred method of tissue freezing; 2) the use of Histogene stain improved cell identification during laser capture; 3) the LCM instrument parameters required for selective podocyte capture were identified; and 4) RNA quality obtained from the LCM samples was suboptimal. These results indicate that the possibility of using LCM for regional podocyte isolation and gene expression analysis is quite promising, and further optimization of the technique will likely yield an important new method for the study of kidney disease pathogenesis.

Keloid disease (KD) is a cutaneous fibroproliferative tumour characterised by heterogeneity, locally aggressive invasion and therapeutic resistance. Clinical, histological and molecular differences between the keloid scar centre and margin as well as recent evidence of the importance of epithelial-mesenchymal interactions (EMI) in KD pathobiology contribute to the complexity and diversity of KD, which coupled with the lack of a validated animal model have hindered research and effective management. Despite significant progress in the field of KD research, reliance on conventional monolayer cell culture and whole tissue analysis methods have failed to fully reflect the natural architecture, pathology and complexity of KD in vivo. In order to address these challenges, a site-specific in situ approach was therefore employed here for the first time in KD research. The first aim of this work was to compare the value of this contemporary approach with traditional methods of tissue dissection. The second aim was to compare the genomic expression between well-defined, distinct keloid sites and normal skin (NS). The third aim was to develop and explore hypotheses arising from this site-specific gene expression profiling approach, so as to enhance understanding of KD pathobiology as a basis for improved diagnostic and therapeutic strategies in future KD management. The fourth aim was to probe these hypotheses with relevant functional in vitro studies. The current site-specific in situ approach was achieved through a combination of laser capture microdissection and whole genome microarray, allowing separation of epidermis from dermis for keloid centre, margin and extralesional sites compared with NS. This in situ approach yielded selective, accurate and sensitive data, exposing genes that were overlooked with alternative methods of dissection. Identification of significant upregulation of the aldo-keto reductase enzyme AKR1B10 in all three sites of the keloid epidermis (KE) in situ, implicated dysregulation of the retinoic acid (RA) pathway in KD pathogenesis. This hypothesis was supported by showing that induced AKR1B10 overexpression in NS keratinocytes reproduced the keloid RA pathway expression pattern. Moreover, co-transfection with a luciferase reporter plasmid revealed reduced RA response element activity. Paracrine signals released by AKR1B10-overexpressing keratinocytes into conditioned medium resulted in TGFβ1 and collagen upregulation in keloid fibroblasts, suggesting the disturbed RA metabolism exerts a pro-fibrotic effect through pathological EMI, thus further supporting the hypothesis of RA deficiency in KE. Gene expression profiling further revealed an upregulation of NRG1 and ErbB2 in keloid margin dermis. Exogenous NRG1 led to enhanced keloid fibroblast migration with increased Src and PTK2 expression, which were attenuated with ErbB2 siRNA studies. Together with the observed failure to recover this expression with NRG1 treatment, suggested the novel KD pathobiology hypothesis that NRG1/ErbB2/Src/PTK2 signaling plays a role in migration at the keloid margin. In addition to these hypotheses, LCM methodology with comprehensive analysis of the data permitted the development of additional novel working hypotheses that will inform future KD research, including inflammatory gene dysregulation and cancer-like stem cells that may contribute to the therapeutic resistance characteristic of KD.

Morphological studies have shown pathology of neurons and glia in many brain disorders, including psychiatric disorders such as major depression. However, most biochemical characterizations of postmortem human brain tissue have not made a distinction between neurons and glia. Laser capture microdissection (LCM) to isolate specific cell types has the potential to advance our understanding of human brain pathologies. Here, RT-PCR was used to evaluate the utility of LCM in the capture of noradrenergic neurons, astrocytes and oligodendrocytes from the locus coeruleus (LC) of postmortem human brain. The 3 LC cell types were individually identified using modifications of established histological and morphological methods. LCM settings were optimized for each cell type and captured cell bodies were those having no nearby cell body of a different phenotype. LC neurons (200), astrocytes (500), and oligodendrocytes (500) were captured within the LC from 3 postmortem brains. RNA was isolated, reversed transcribed, and markers for neurons (tyrosine hydroxylase [TH], dopamine beta-hydroxylase [DBH]), astrocytes (glial fibrillary acidic protein [GFAP]), and oligodendrocytes (myelin oligodendrocyte glycoprotein [MOG]), along with 3 references (actin, GAPDH, ubiquitin C) were PCR amplified and quantified by standardized end-point PCR. RNA quality as assessed by RIN was not altered by LCM as compared to RNA isolated from homogenized tissue. TH gene expression was found only in neurons in 2 of the 3 brains. DBH gene expression was ~5-fold greater in neurons than in astrocytes and oligodendrocytes. GFAP gene expression in astrocytes was 7- and 5-fold greater than that in neurons and oligodendrocytes, respectively. MOG gene expression was only detected in oligodendrocytes. Different expression ratios of marker genes between neurons and glia suggest that simple cross contamination of mRNA is unlikely. Glial cells may contain DBH mRNA. Alternatively, DBH, but not TH, mRNA may occur in neuronal dendrites or axons in close association with glial cells that become captured with glia during LCM. GFAP may be expressed in low levels in neurons and oligodendrocytes, or alternatively, GFAP mRNA may be located in astrocytic processes in close association with neuronal and oligodendrocyte cell bodies. Use of a single marker to identify a cell type may be insufficient; other cell types for comparison or additional markers may be required. Multiple well-characterized markers can be used to evaluate clarity of cell capture for each sample. With due regard for specific limitations, LCM can be used to evaluate the molecular pathology of specific cell types in postmortem human brain.

No description available.

No description available.

Laser capture microdissection (LCM) is a versatile computer-assisted dissection method that permits collection of tissue samples with a remarkable level of anatomical resolution. LCM's application to the study of human brain pathology is growing, although it is still relatively underutilized, compared with other areas of research. The present study examined factors that affect the utility of LCM, as performed with an Arcturus Veritas, in the study of gene expression in the human brain using frozen tissue sections. LCM performance was ascertained by determining cell capture efficiency and the quality of RNA extracted from human brain tissue under varying conditions. Among these, the relative humidity of the laboratory where tissue sections are stained, handled, and submitted to LCM had a profound effect on the performance of the instrument and on the quality of RNA extracted from tissue sections. Low relative humidity in the laboratory, i.e., 6-23%, was conducive to little or no degradation of RNA extracted from tissue following staining and fixation and to high capture efficiency by the LCM instrument. LCM settings were optimized as described herein to permit the selective capture of astrocytes, oligodendrocytes, and noradrenergic neurons from tissue sections containing the human locus coeruleus, as determined by the gene expression of cell-specific markers. With due regard for specific limitations, LCM can be used to evaluate the molecular pathology of individual cell types in post-mortem human brain.