Identification des mécanismes mutagènes liés aux facteurs de risque et aux processus cellulaires dans les cancers du foie

Cancer is a disease of the genome. A normal cell goes rogue and is transformed into a cancerous cell due to acquired somatic mutations in its genome. The catalogue of these somatic mutations observed in the cancer genome is the outcome of multiple mutational processes that have been operative over the lifetime of a patient. These mutational processes that have occurred throughout the development of cancer may be infidelity of the DNA replication machinery, impaired DNA repair system, enzymatic modifications of DNA, or exposures to exogenous or endogenous mutagens. Each mutational process leaves a characteristic pattern – a “mutational signature” on the cancer genome. Various genomic features related to genome architecture, including DNA replication and transcription, modulate these mutational processes. During my PhD, I analyzed whole exome and whole genome sequencing data from liver tumors to understand the mutational processes remodeling these tumor genomes, their interaction with risk factors, cellular processes, and driver genes, and their evolution along the tumor histories. For that aim, I used existing statistical methods and I developed innovative computational tools to:-extract mutational and structural variant signatures from next-generation sequencing data-identify risk factors or genetic alterations underlying each process-predict the mutational process at the origin of each somatic mutation-explore correlations between mutation rates and cellular processes like replication and transcription-reconstruct the clonal history of a tumor and the timing of mutational processes and copy-number changes These innovative analytical strategies allowed me to identify 10 mutational signatures: 5 ubiquitous signatures operative in every liver cancer but modulated by risk factors (gender, alcohol, tobacco), and 5 sporadic signatures operative in <5% of HCC and associated with specific known (aflatoxin B1, aristolochic acid) or unknown mutational processes. I also identified 6 structural variant signatures, including striking duplicator or deletor phenotypes in rare tumors. Each mutational process showed a different relationship with replication and transcription. Signatures of bulky DNA adducts (polycyclic aromatic hydrocarbons, aflatoxin B1, aristolochic acid) strongly decreased in highly expressed genes due to transcription-coupled repair, whereas the alcohol-related signature 16 displayed a unique feature of transcription-coupled damage. A striking positive correlation between indel rate and gene expression was observed, leading to recurrent mutations in very highly expressed tissue-specific genes. Finally, reconstructing the clonal history of HCC revealed the evolution of mutational processes along tumor development and identified synchronous chromosome duplications as late events probably leading to fast tumor growth and clinical detection of the tumor. Together, these findings shed new light on the mechanisms generating DNA alterations along the natural history of liver cancers.Le cancer est une maladie du génome. La transformation tumorale résulte de l’acquisition de mutations somatiques via divers processus mutagènes opérant tout au long de la vie du patient. Les mécanismes à l’origine des mutations incluent les erreurs de réplication, les défauts de réparation de l’ADN, les modifications de base spontanées ou catalysées par des enzymes cellulaires, et l’exposition à des agents mutagènes endogènes (ROS) ou exogènes (tabac, UV…). Au cours de ma thèse, j’ai analysé des données de séquençage exome et génome complet de tumeurs hépatiques pour décortiquer les mécanismes à l’origine des mutations dans ces tumeurs, leur interaction avec les facteurs de risque, les processus cellulaires, les gènes drivers, et leur évolution au cours de la maladie. J’ai utilisé des méthodes statistiques existantes et dévoloppé des outils bioinformatiques innovants pour:-extraire les signatures de mutations et de réarrangements structuraux à l’aide de données de séquençage à haut débit-identifier les facteurs de risque et/ou les altérations génétiques à l’origine de chacune-prédire les mécanismes mutagènes à l’origine de chaque mutation somatique-explorer les corrélations entre la densité des mutations et les processus cellulaires comme la réplication et la transcription-reconstruire l’histoire clonale des tumeurs et dater l’apparition des signatures mutationnelles et des aberrations chromosomiques.Ces approches innovantes m’ont permis d’identifier 10 signatures mutationnelles: 5 signatures ubiquitaires à l’œuvre dans toutes les tumeurs hépatiques mais modulées par les facteurs de risque (sexe, alcool, tabac), et 5 signatures sporadiques opérant dans moins de 5% des tumeurs et associées à des étiologies connues (aflatoxine B1, acide aristolochique) ou restant à identifier. J’ai aussi mis en évidence 6 signatures de réarrangements structuraux, notamment des phénotypes duplicateurs et déléteurs, spécifiques de petits groupes de tumeurs. Chaque processus mutagène est modulé différemment par la réplication et la transcription. Les signatures liées à des molécules formant des adducts sur l’ADN (hydrocarbures polycycliques aromatiques, aflatoxine B1, acide aristolochique) sont nettement moins actives dans les gènes fortement exprimés suite à l’action du transcription-coupled repair, alors que la signature 16, liée à l’alcool, présente un motif unique de transcription-coupled damage. Une corrélation étonnante entre la densité des petites insertions et délétions (indels) et l’expression des gènes a été identifiée, conduisant à une accumulation considérable d’indels dans les gènes très forterment exprimés dans les cellules hépatiques. Enfin, l’histoire clonale des tumeurs hépatiques montre l’évolution des signatures mutationnelles au cours du temps et identifie l’accumulation de gains chromosomiques multiples comme un évènement tardif entraînant probablement une croissance de la tumeur jusqu’à une taille détactable en clinique. Ces résultats nous éclairent sur les mécanismes à l’origine des altérations génomiques dans l’histoire naturelle des cancers du foie

The In-vitro studies and evaluation of telmisartan marketed tablets

Tablets or capsules taken orally remain one of the most effective means of treatment available. The effectiveness of such dosage forms relies on the drug dissolving in the fluids of the gastrointestinal tract prior to absorption into the systemic circulation. The present study reveals the evaluation of four marketed sample of Telmisartan tablets. The main aim of the study is to conduct dissolution test on the tablets to determine the compliance with a given official monograph. Four different marketed samples of Telmisartan were purchased from local market. The Telmisartan tablets were evaluated for the various in-vitro tablet properties such as thickness, hardness, friability, weight variation, drug content, disintegration time and dissolution rate. In-vitro dissolution test is conducted on four different brands of telmisartan tablets to assess their equivalency. All the four marketed samples of Telmisartan have shown good tablet properties and comply with the pharmacopoeial specification. The in- vitro dissolution showed the 80% drug release within one hour from all the four brands which complies with the specification of pharmacopoeia

Mutational signatures reveal the dynamic interplay of risk factors and cellular processes during liver tumorigenesis

Tumorigenesis is a complex process driven by numerous risk factors. Here, genomic analysis of liver cancer reveals the evolution of mutational signatures during tumor development, highlighting mutational and structural signatures linked to environmental exposures and endogenous cellular processes

Cyclin A2/E1 activation defines a hepatocellular carcinoma subclass with a rearrangement signature of replication stress

Cyclins A2 and E1 are known to regulate the cell cycle by promoting S phase entry and progression. Here, they identify an aggressive hepatocellular carcinoma subgroup exhibiting cyclin activation through various mechanisms and find this subgroup to display replication stress-induced structural rearrangements frequently activating TERT promoter

Imaging-AMARETTO: An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes.

The availability of increasing volumes of multiomics, imaging, and clinical data in complex diseases such as cancer opens opportunities for the formulation and development of computational imaging genomics methods that can link multiomics, imaging, and clinical data.Here, we present the Imaging-AMARETTO algorithms and software tools to systematically interrogate regulatory networks derived from multiomics data within and across related patient studies for their relevance to radiography and histopathology imaging features predicting clinical outcomes. RESULTS To demonstrate its utility, we applied Imaging-AMARETTO to integrate three patient studies of brain tumors, specifically, multiomics with radiography imaging data from The Cancer Genome Atlas (TCGA) glioblastoma multiforme (GBM) and low-grade glioma (LGG) cohorts and transcriptomics with histopathology imaging data from the Ivy Glioblastoma Atlas Project (IvyGAP) GBM cohort. Our results show that Imaging-AMARETTO recapitulates known key drivers of tumor-associated microglia and macrophage mechanisms, mediated by STAT3, AHR, and CCR2, and neurodevelopmental and stemness mechanisms, mediated by OLIG2. Imaging-AMARETTO provides interpretation of their underlying molecular mechanisms in light of imaging biomarkers of clinical outcomes and uncovers novel master drivers, THBS1 and MAP2, that establish relationships across these distinct mechanisms. CONCLUSION Our network-based imaging genomics tools serve as hypothesis generators that facilitate the interrogation of known and uncovering of novel hypotheses for follow-up with experimental validation studies. We anticipate that our Imaging-AMARETTO imaging genomics tools will be useful to the community of biomedical researchers for applications to similar studies of cancer and other complex diseases with available multiomics, imaging, and clinical data.journal article2020 MayimportedSupported by the National Cancer Institute (NCI) Informatics Technology for Cancer Research (R21CA209940 [O.G., T.F.B., J.P.M., N.P.], U01CA214846 [V.C.], U01CA214846 Collaborative Set-aside [O.G., A.M.K., V.C., N.P.], U24CA194107 [J.P.M.], U24CA220341 [J.P.M.], U24CA180922 [B.J.H., N.P., A. Regev]), NCI (R01CA215072 [A.M.K.], U01CA217851 [O.G.], U01CA199241 [O.G.], Stanford CTD2 [O.G.]), National Institute of Allergy and Infectious Diseases (R03AI131066 [T.F.B., N.P.]), and National Institute of Biomedical Imaging and Bioengineering (R01EB020527 [O.G.]). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health

Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets.

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Nestin as a Diagnostic and Prognostic Marker for Combined Hepatocellular-Cholangiocarcinoma.

International audienceBACKGROUND AND AIMS: Combined Hepatocellular-Cholangiocarcinoma (cHCC-CCA) is a rare primary liver cancer (PLC) associated with a poor prognosis. Given the challenges in its identification and its clinical implications, biomarkers are critically needed. We aimed to investigate the diagnostic and prognostic value of the immunohistochemical expression of Nestin, a progenitor cell marker, in a large multicentric series of PLC. METHODS: We collected 461 cHCC-CCA samples from 32 different clinical centers. Control cases included 368 hepatocellular carcinomas (HCC) and 221 intrahepatic cholangiocarcinomas (ICCA). Nestin immunohistochemistry was performed on whole tumor sections. Diagnostic and prognostic performances of Nestin expression were determined using receiver operating characteristic curves and cox regression modeling. RESULTS: Nestin was able to distinguish cHCC-CCA from HCC with AUC of 0.85 and 0.86 on surgical and biopsy samples, respectively. Performance was lower for the distinction of cHCC-CCA from ICCA (AUC of 0.59 and 0.60). Nestin, however, showed a high prognostic value, allowing identification of the subset of cHCC-CCA ("Nestin High", >30% neoplastic cells with positive staining) associated with the worst clinical outcome (shorter disease-free and overall survival) after surgical resection and liver transplantation, as well as when assessment was performed on biopsies. CONCLUSION: We show in different clinical settings that Nestin has a diagnostic value and that it is a useful biomarker to identify the subset of cHCC-CCA associated with the worst clinical outcome. Nestin immunohistochemistry may be used to refine risk stratification and improve treatment allocation for patients with this highly aggressive malignancy. LAY SUMMARY: Combined Hepatocellular-Cholangiocarcinoma (cHCC-CCA) is a rare primary liver cancer (PLC) that lacks robust tissue biomarkers. We show in different clinical settings that Nestin immunohistochemical staining has a diagnostic value and is a useful biomarker to identify the subset of cHCC-CCA associated with the worst clinical outcome. Nestin immunohistochemistry may be used to refine risk stratification and improve treatment allocation for patients with this highly aggressive malignancy

Nestin as a diagnostic and prognostic marker for combined hepatocellular-cholangiocarcinoma

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