1. Antibody Mediated Rejection and T-cell Mediated Rejection Molecular Signatures Using Next-Generation Sequencing in Kidney Transplant Biopsies.
- Author
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Cortes Garcia E, Giarraputo A, Racapé M, Goutaudier V, Ursule-Dufait C, de la Grange P, Adoux L, Raynaud M, Couderau C, Mezine F, Dagobert J, Bestard O, Moreso F, Villard J, Halleck F, Giral M, Brouard S, Danger R, Gourraud PA, Rabant M, Couzi L, Le Quintrec M, Kamar N, Morelon E, Vrtovsnik F, Taupin JL, Snanoudj R, Legendre C, Anglicheau D, Budde K, Lefaucheur C, Loupy A, and Aubert O
- Subjects
- Humans, Biopsy, Male, Female, Middle Aged, Adult, Gene Expression Profiling, Transcriptome, Kidney pathology, Sequence Analysis, RNA, Aged, Kidney Transplantation, Graft Rejection genetics, Graft Rejection immunology, High-Throughput Nucleotide Sequencing, T-Lymphocytes immunology
- Abstract
Recently, interest in transcriptomic assessment of kidney biopsies has been growing. This study investigates the use of NGS to identify gene expression changes and analyse the pathways involved in rejection. An Illumina bulk RNA sequencing on the polyadenylated RNA of 770 kidney biopsies was conducted. Differentially-expressed genes (DEGs) were determined for AMR and TCMR using DESeq2. Genes were segregated according to their previous descriptions in known panels (microarray or the Banff Human Organ Transplant (B-HOT) panel) to obtain NGS-specific genes. Pathway enrichment analysis was performed using the Reactome and Kyoto Encyclopaedia of Genes and Genomes (KEGG) public repositories. The differential gene expression using NGS analysis identified 6,141 and 8,478 transcripts associated with AMR and TCMR. While most of the genes identified were included in the microarray and the B-HOT panels, NGS analysis identified 603 (9.8%) and 1,186 (14%) new specific genes. Pathways analysis showed that the B-HOT panel was associated with the main immunological processes involved during AMR and TCMR. The microarrays specifically integrated metabolic functions and cell cycle progression processes. Novel NGS-specific based transcripts associated with AMR and TCMR were discovered, which might represent a novel source of targets for drug designing and repurposing., Competing Interests: Author PG was employed by GenoSplice. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Cortes Garcia, Giarraputo, Racapé, Goutaudier, Ursule-Dufait, de la Grange, Adoux, Raynaud, Couderau, Mezine, Dagobert, Bestard, Moreso, Villard, Halleck, Giral, Brouard, Danger, Gourraud, Rabant, Couzi, Le Quintrec, Kamar, Morelon, Vrtovsnik, Taupin, Snanoudj, Legendre, Anglicheau, Budde, Lefaucheur, Loupy and Aubert.)
- Published
- 2024
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