Biology subjects

Debbagh, C.

Publications and source records attributed to Debbagh, C..

3 recordsLinked to original sources

bioRxiv2025

Characterization of Immunoglobulin Loci in Pongo abelii and Pongo pygmaeus: Insights from Multi-Genome Annotation and IMGT-Based Curation

Antibodies, or immunoglobulins (IG), are central to the vertebrate adaptive immune system, yet the genomic architecture of IG loci remains poorly characterized in many nonhuman primates. In this study we present the first comprehensive genomic analysis of the immunoglobulin (IG) loci (IGH, IGL, and IGK) in two critically endangered orangutan species; Pongo abelii (Sumatran orangutan) and Pongo pygmaeus (Bornean orangutan) across multiple genome assemblies. Using IMGT-standardized biocuration framework combined with read-level structural validation, we identified previously undocumented haplotype-specific variation, including multigene duplications, asymmetric gene absence, and species-specific expansions of variable gene families. Recombination signal sequence (RSS) and switch region analyses revealed conserved regulatory motifs with potential implications for V(D)J recombination and class-switch recombination. These findings underscore the complexity and evolutionary adaptability of IG loci in great apes and highlight the value of orangutans as key references for understanding immune system evolution in the Hominidae lineage.

immunology↗

bioRxiv2025

IMGT(R) at scale: FAIR, Dynamic and Automated Tools for Immune Locus Analysis

IMGT(R), the international ImMunoGeneTics information system(R), has advanced its comprehensive platform for the analysis of immunoglobulin (IG) and T cell receptor (TR) genes through the development of new automated and scalable tools. This article presents major updates aligned with IMGTs three axes of research. Axis I introduces dynamic resources such as IMGT/GeneTables, IMGT/AssemblyComparison, and IMGT/StatAssembly, enabling real-time access to annotated genomic data and quality assessment of assemblies. Axis II enhances repertoire analysis with a redesigned IMGT/GeneFrequency tool and new customization features in IMGT/V-QUEST, supporting flexible exploration of IG and TR gene expression. Axis III improves the accurate prediction of peptide-MHC thanks to IMGT/RobustpMHC. Additionally, the IMGT Knowledge Graph (IMGT-KG) and its therapeutic extension, IMGT/mAb-KG, provide semantically structured access to more than 100 million immunogenetic triplets, integrating IMGT databases and linking IMGT content to external biomedical resources. These developments promote standardization, interoperability, and integrative analysis across immunogenetics and clinical applications, reinforcing IMGTs role as a core reference in the era of FAIR data and personalized medicine.

bioinformatics↗

bioRxiv2024

Deciphering of Gorilla gorilla gorilla Immunoglobulin Loci in Multiple Genome Assemblies and Enrichment of IMGT Resources

Through the analysis of immunoglobulin genes at the IGH, IGK, and IGL loci from four Gorilla gorilla gorilla genome assemblies, IMGT(R) provides an in-depth overview of these loci and their individual variations in a species closely related to humans. The similarity between gorilla and human IG gene organization allowed the assignment of gorilla IG gene names based on their human counterparts. This study revealed significant findings, including variability in the IGH locus, the presence of known and new copy number variations (CNVs), and the accurate estimation of IGHG genes. The IGK locus displayed remarkable homogeneity and lacked the gene duplication seen in humans, while the IGL locus showed a previously unconfirmed CNV in the J-C cluster. The curated data from these analyses, available on the IMGT website, enhance our understanding of gorilla immunogenetics and provide valuable insights into primate evolution.

genomics↗