Abstract
Background & Aims CD8+ T-cell gene expression has been implicated in the pathogenesis of Inflammatory Bowel Diseases (IBD) and has been shown to correlate with disease outcome in adult patients. Moreover, CD8+ T-cell exhaustion was identified as a contributing mechanism that impacts on disease behaviour. We aimed to explore CD8+ T-cell gene expression and DNA methylation in children newly diagnosed with IBD and test their correlation with disease outcome.
Methods We prospectively recruited 112 children with IBD at the point of diagnosis and 19 non-IBD controls. Follow-up samples were obtained from a subset of patients at 3-month intervals (n=62). CD8+ T-cells were purified from peripheral blood samples using magnetic bead sorting and genome-wide transcriptional (n=192) and DNA methylation (n=66) profiles were generated using Affymetrix and Illumina arrays respectively. Publicly available adult CD8+ T-cell transcriptomes and DNA methylomes were included in data analyses to investigate age dependant differences.
Results Variation amongst CD8+ T-cell transcriptomes obtained from children showed association with disease, systemic inflammation, age and gender but lacked correlation with disease outcome in pediatric IBD. In contrast to CD8+ T-cell transcriptomes in adult Crohn’s Disease (CD), samples from pediatric patients did not show variation within genes forming part of the previously reported prognostic expression or T-cell exhaustion signatures. Pediatric CD patient derived DNA methylation profiles also lacked correlation with disease outcome but in comparison to adult CD8+ methylomes showed a higher predicted proportion of CD8+ naïve T-cells.
Conclusions Our findings indicate age-related differences in IBD pathogenesis and highlight the importance of validating adult clinical biomarkers in pediatric cohorts.
Footnotes
Grant support: This study was supported by grants from the Broad Medical Research Program at Crohn’s and Colitis Foundation of America (BMRP, CCFA), Isaac Newton Trust / Wellcome Trust ISSF and University of Cambridge Joint Research Grant Scheme, Cambridge Biomedical Research Campus (BRC) pump priming grant and Action Medical Research UK. MG was supported by fellowships from the Crohn’s in Childhood Research Association (CICRA) charity, the European Society for Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN) and the IG-IBD International Exchange Program. DZ and RDE were supported by core funding from the European Molecular Biology Laboratory (EMBL).
The authors would like to thank Natalia Savinykh Yarkoni at the at NIHR Cambridge BRC Cell Phenotyping Hub for her support with cell sorting. Furthermore, we express our gratitude towards all patients and their parents who have participated in this study. We thank Bella’s Fund for their support and contribution towards raising awareness for childhood IBD and charity funding for the project. We would like to thank pediatric anaesthetists at Cambridge University Hospitals for their help with obtaining blood samples from patients. We are also very grateful for the helpful discussions and guidance on data analysis provided by Theo Bammler and James MacDonald The University of Washington Department of Environmental and Occupational Health Sciences, USA. Lastly, the authors express their gratitude to Paul Lyons (University of Cambridge, Department of Medicine) for his support in obtaining funding for the project and providing advice on data analyses.
Disclosures: The authors declare no conflict of interest.
Transcript and DNA methylation Profiling: All generated array data have been deposited in ArrayExpress, accession E-MTAB-7923 (gene transcription arrays), and XXXX-submitted (DNA methylation data).
Writing Assistance: None
Abbreviations
- AAV
- Anca Associated Vasculitis
- CD
- Crohn’s Disease
- CpG
- Cytosine – phosphate - Guanine
- DEG
- differentially expressed gene
- DNAm
- DNA methylation
- IBD
- Inflammatory Bowel Disease
- MACS
- Magnetic Activated Cell Sorting
- PBMC
- Peripheral Blood Mononuclear Cells
- PCDAI
- Pediatric Crohn’s Disease Activity Index
- PDCD1
- Programmed Cell Death 1
- PUCAI
- Pediatric Ulcerative Colitis Activity Index
- PC
- Principle Component
- SLE
- Systemic Lupus Erythematosus
- UC
- Ulcerative Colitis
- WGCNA
- weighted gene co-expression network analysis