A RAGHUBAR1,2, D PHAM1, X TAN1, L GRICE1, P Y LAM1, J CRAWFORD1, S ANDERSEN1, S HOLLAND1, A STEWART2, L FRANCIS2, A COMBES3, A KASSIANOS4, H HEALY5, Q NGUYEN1, A MALLETT1,5
1The University of Queensland, 2Anatomical Pathology, Pathology Queensland, 3Monash University , 4Chemical Pathology, Pathology Queensland, 5The Royal Brisbane and Women’s Hospital Metro North HHS
Aim: To develop a pipeline for precision diagnostics in mammalian kidney integrating novel spatial transcriptomics molecular profiles with traditional histomorphology.
Background: Advances in sequencing methods have increased available molecular information on dissociated cells and tissues. Spatially linking this molecular information with histomorphology is needed to understand a complex organ like the kidney, in both health and disease.
Methods: Here we used the commercially available 10x Genomics ST platform to investigate the spatially resolved transcriptome expressions in late fetal (n=2), young adult male (n=3) and female (n=3) mouse frozen kidney, and healthy human (n=4) cortical frozen kidney tissue sections. We utilised Space Ranger (10x Genomics), Seurat and stLearn analysis pipelines to explore the spatial transcriptome expression within the kidney tissue sections.
Results: We identified a unique transcriptome plasticity in late fetal mouse, young adult mouse and healthy human cortical kidney tissue. Further dimensional reduction identified transcriptome clusters which correlated with distinct developing kidney structures in fetal mouse kidney tissues, functional cortical and medulla regions in young adult mouse kidney tissues and key structural and functional components of the nephron in human cortical kidney tissues.
Conclusion: ST is a non-dissociative sequencing and imaging method which allows molecular profiles to be integrated with histomorphology of frozen kidney tissue sections. This provides a novel precision diagnostics tool to elucidate physiological and non-physiological conditions at the cell-to-cell, nephron and tissue level in mammalian kidney.
Arti Raghubar is a clinical scientist with a special interest in renal cancer and molecular histology. After graduating from Queensland University of Technology with a BAppSci (MedSci) she completed training in a private histology laboratory in Brisbane. She has also completed a MMolBiol (The University of Queensland) investigating micro-proteomics in Immunoglobulin A Nephropathy. She currently works as a clinical scientist at Anatomical Pathology, Pathology Queensland at The Royal Brisbane and Women’s Hospital. She is also undertaking a PhD in renal cancer and the application of multi-omics profiling at the Institute for Molecular Bioscience, The University of Queensland.