Orthogonal Comparison of Molecular Signatures of Kidney Transplants With Subclinical and Clinical Acute Rejection: Equivalent Performance Is Agnostic to Both Technology and Platform

Abstract

We performed orthogonal technology comparisons of concurrent peripheral blood and biopsy tissue samples from 69 kidney transplant recipients, who underwent a comprehensive algorithm-driven clinical phenotyping. The sample cohort included patients with normal protocol biopsies and stable transplant function (TX, n=25), subclinical acute rejection (subAR, n=23), and clinical acute rejection (cAR, n=21). Comparisons between microarray and RNA sequencing (RNA-seq) signatures were performed, demonstrating a strong correlation between the blood and tissue compartments for both technology platforms. A number of shared differentially expressed genes and pathways between subAR and cAR in both platforms strongly suggest that these two clinical phenotypes form a continuum of alloimmune activation. SubAR is associated with fewer or less expressed genes than cAR in blood, whereas in biopsy tissues, this clinical phenotype demonstrates a more robust molecular signature for both platforms. The discovery work done in this study confirms a clear ability to detect gene expression profiles for TX, subAR and cAR in both blood and biopsy tissue, yielding equivalent predictive performance, that is agnostic to either technology or platform. Our data also provide strong biologic insights into the molecular mechanisms underlying these signatures, underscoring their logistical potential as molecular diagnostics to improve clinical outcomes following kidney transplantation.

Review: The transcripts associated with organ allograft rejection

“…14 We estimate that RNAseq needs >60 million "mappable" reads to capture the relatively low expression mRNAs that are most specific for rejection (eg, CTLA4, IFNG), increasing costs and time compared to microarrays. 14 We estimate that RNAseq needs >60 million "mappable" reads to capture the relatively low expression mRNAs that are most specific for rejection (eg, CTLA4, IFNG), increasing costs and time compared to microarrays.…”

“…One report found that microarrays and RNAseq have the ability to develop similar signatures of rejection in kidney transplant patients, although the sample size was small and the depth of sequencing was low. 14 We estimate that RNAseq needs >60 million "mappable" reads to capture the relatively low expression mRNAs that are most specific for rejection (eg, CTLA4, IFNG), increasing costs and time compared to microarrays. RNAseq is not suited for routine diagnostics but is ideal for research and discovery as the alternative mRNA splicing and alternative promoters add intriguing levels of complexity and potential specificity that have not yet been explored.…”

Results of Questionnaire Survey of Current Immune Monitoring Practice of Transplant Clinicians and Clinical Pathologists in Korea: Basis for Establishment of Harmonized Immune Monitoring Guidelines

“…However, luminex bead technologies used for the detection of antibodies in antigen, allele or epitope levels for HLA (7)(8)(9) and non-HLA systems (15), and molecular technologies to detect transcript signatures of diverse immunologic changes are broadening our choice of tests (16)(17)(18).…”

Late graft failure after kidney transplantation as the consequence of late versus early events

“…4,31 Critical to these efforts will be improved noninvasive monitoring tools to enable recognition of new graft injury before it is clinically evident. 35,36 Though, given relative inefficacy of current therapeutic interventions, some might question the benefit of more intense long-term monitoring, we would counter that new therapies can emerge only with timely, proper diagnosis.…”