A5071155350- Genomics and Chromatin Dynamics
- Immunotherapy and Immune Responses
- vaccines and immunoinformatics approaches
- DNA Repair Mechanisms
- SARS-CoV-2 and COVID-19 Research
- Bioinformatics and Genomic Networks
- Epigenetics and DNA Methylation
- SARS-CoV-2 detection and testing
- Gene expression and cancer classification
- Glycosylation and Glycoproteins Research
- Chromosomal and Genetic Variations
- CRISPR and Genetic Engineering
- RNA modifications and cancer
- Animal Virus Infections Studies
- Cardiac Arrest and Resuscitation
- Fractal and DNA sequence analysis
- Monoclonal and Polyclonal Antibodies Research
- Multiple Myeloma Research and Treatments
- Cancer Immunotherapy and Biomarkers
- Trauma and Emergency Care Studies
- Cancer Genomics and Diagnostics
- Emergency and Acute Care Studies
- Viral Infections and Vectors
- Viral Infections and Immunology Research
- T-cell and B-cell Immunology
Lebanese American University
2020-2022
Centre Léon Bérard
2022
Laboratoire de Physique de l'ENS de Lyon
2013-2017
Institut de Recherche en Cancérologie de Montpellier
2017
École Normale Supérieure de Lyon
2013-2017
Université Claude Bernard Lyon 1
2013-2015
Centre National de la Recherche Scientifique
2013-2015
Human endogenous retroviruses (HERVs) represent 8% of the human genome. HERV products may tumor antigens relevant for cancer immunotherapy. We developed a bioinformatic approach to identify shared CD8 + T cell epitopes derived from cancer-associated HERVs in solid tumors. Six candidates among most commonly HLA-A2 with evidence translation were selected immunological evaluation. In vitro priming assays confirmed immunogenicity these epitopes, which induced high-avidity clones. These cells...
Abstract The cell intrinsic antiviral response of multicellular organisms developed over millions years and critically relies on the ability to sense eliminate viral nucleic acids. Here we use an affinity proteomics approach in evolutionary distant species (human, mouse fly) identify proteins that are conserved their associate with diverse This shows a core orthologous targeting genetic material species-specific interactions. Functional characterization influence 181 candidates replication 6...
We use graph theory to analyze chromatin interaction (Hi-C) data in the human genome. show that a key functional feature of genome---``master'' replication origins---corresponds DNA loci maximal network centrality. These form set interconnected hubs both within chromosomes and between different chromosomes. Our results open way fruitful concepts decipher structural organization relation genome functions such as transcription. This quantitative information should prove useful discriminate...
Abstract Human endogenous retroviruses (HERVs) represent 8% of the human genome. The expression HERVs and their immune impact have not been extensively studied in Acute Myeloid Leukemia (AML). In this study, we used a reference 14 968 HERV functional units to provide thorough analysis normal AML bone marrow cells. We show that retrotranscriptome accurately characterizes leukemic cell subpopulations, including leukemia stem cells, line with different epigenetic profiles. then delineates...
The three-dimensional (3D) architecture of the mammalian nucleus is now being unraveled thanks to recent development chromatin conformation capture (3C) technologies. Here we report results a combined multiscale analysis genome-wide mean replication timing and data that reveal some intimate relationships between folding human DNA replication. We previously described megabase N/U-domains as multiorigin units, showed their borders are 'master' initiation zones likely initiate cascades origin...
Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological challenge for computational biology which consists in objectively extracting from these data the structural motifs characteristic of organisation.We deployed fast multi-scale community mining algorithm based on spectral graph wavelets characterise networks intra-chromosomal interactions...
Abstract Cancer cells rely on alternative modes of translation for protein synthesis, promoting internal ribosome entry site (IRES)-dependent mRNA encoding pro-oncogenic factors. Furthermore, ribosomes translate with lower fidelity in tumor cells. We proposed that these translational modifications cancer produce shared tumor-specific epitopes derived from IRES-containing oncogenes. To identify such neoepitopes, we developed an silico -based method applied to c-MYC . showed the non-canonical...
Abstract Background Ovarian cancer represents the most lethal gynecological with poor results of checkpoint inhibitors. Human endogenous retroviruses (HERVs) are aberrantly expressed by tumor cells and may represent a source shared T cell epitopes for immunotherapy regardless mutational burden. Methods A transcriptomic analysis based on RNA-sequencing (RNA-seq) was developed to quantify expression HERV-K sequences containing selected epitopes. The presence HERV-K/HML-2 Gag antigen then...
The world has been dealing with the SARS-COV-2 pandemic since December 2019 and a lot of effort focused on tracking spread virus by gathering information regarding testing statistics generating viral genomic sequences. Unfortunately, there is neither single comprehensive resource global historical data nor centralized database summary identified variants. We merged different pre-aggregated complemented them our manually extracted ones, which consist 6852 test from 76 countries/states...
We review the existence of a new type megabase-sized replication domains along human genome. These are revealed in 7 somatic cell types by U-shaped patterns timing profiles. In germline, these appear as N-shaped DNA compositional asymmetry profiles resulting from replication-associated mutational asymmetries. demonstrated that average fork polarity is directly proportional to both and derivative profile. Hence, changes linear manner across U/N-replication enlightening robust mode during...
Abstract The world has been dealing with the COVID-19 pandemic since December 2019 and a lot of effort focused on tracking spread virus by gathering information regarding testing statistics generating viral genomic sequences. Unfortunately, there is neither single comprehensive resource global historical data nor centralized database summary identified variants.We merged different pre-aggregated complemented them our manually extracted ones, which consist 6852 test from 76 countries/states...
Abstract Introduction: Basic Life Support (BLS) is the rapid detection of cardiac arrest and initial adequate response to maintain ventilation circulation. Multiple studies around world have shown that when used infrequently, BLS skills will deteriorate within 3 6 months after training, even though theoretical knowledge was retained longer. We aim identify differences in training among different physician populations according their age, specialty, area practice provide areas improvements....
Abstract Human endogenous retroviruses (HERVs) represent 8% of the human genome. HERVs are silenced by epigenetic mechanisms in normal cells but aberrantly expressed tumor cells. Given their viral origin, HERV products may antigens relevant for cancer immunotherapy. We developed a systematic bioinformatics-based approach to identify shared CD8+ T cell epitopes derived from cancer-associated solid tumors. Six HLA-A2 among most epitope candidates with evidence translation were selected further...
<h3>Background</h3> Human endogenous retroviruses (HERVs) are aberrantly expressed by tumor cells and may represent a source of T cell epitopes <h3>Methods</h3> Using TCGA pancancer RNAseq data (n=8,893 samples), we developed bioinformatics-based method to select cancer-specific HERVs associated with cytotoxic response ("cyt-HERVs") identify shared epitope candidates. were primed selected short long peptide candidates from HLA-A2+ healthy donors. Peptide-specific dextramers used sort expand...