Characterization of Kidney Allograft Pathology Using the Histomap Gene Expression Profile (GEP) and Formalin Fixed Paraffin Embedded (FFPE) Tissue
1University of Wisconsin Madison, Madison, WI, 2University of Wisconsin, Madison, WI, 3CareDx, Brisbane, CA, 4University of Wsiconsin, Madison, WI
Meeting: 2022 American Transplant Congress
Abstract number: 377
Keywords: Gene expression, Polyma virus, Rejection
Topic: Basic Science » Basic Science » 02 - Acute Rejection
Session Information
Session Time: 5:30pm-7:00pm
Presentation Time: 6:50pm-7:00pm
Location: Hynes Room 309
*Purpose: The new Banff Human Organ Transplant (B-HOT) gene panel assessed on nCounter system has been created through a collaboration between NanoString and the Banff Foundation for Allograft Pathology (https://banfffoundation.org/). The methodology serves to bridge the gap between genome-wide (microarrays) and targeted (real-time quantitative PCR) expression profiling. CareDx designed HistoMap, a robust and highly reproducible method for detecting the expression of 758 genes from the B-HOT panel in a single reaction with high sensitivity and linearity across a broad range of expression levels, using FFPE kidney tissue and NanoString nCounter system. The purpose of this study was to characterize GEP that identify different molecular phenotypes of antibody mediated rejection (ABMR), T-cell mediated rejection (TCMR), and BK virus nephropathy (BKVN) using the HistoMap platform.
*Methods: FFPE kidney allograft tissues from recipients with ABMR (n=53, 24 C4d-positive and 29 C4d-negative), TCMR (n=16), BKVN (n=13) and no rejection (n=12) were analyzed using the HistoMap platform. Patients with mixed pathology were excluded. The B-HOT gene panel was assessed by HistoMap. Differential expression analysis between these 4 groups was performed to calculate fold change (FC), which is calculated from the ratio geomean (condition1)/ geomean (condition 2). If ratio > 1, FC = ratio, else FC = -(1/ratio). Statistical significance was defined at False Discovery Rate-adjusted p-value of <0.05.
*Results: A large number of genes included in the B-HOT panel were strongly upregulated (FC≥2) in active-ABMR (n=158), TCMR (n=213) and BKVN (n=241). 29 genes were identified that are strongly upregulated in TCMR, compared to active ABMR (CXCL13 (FC=9.8), LTF (6.4), CCL18 (5.4), LAG3 (4.7), MS4A1 (4.4), SELL (4.3), CTLA4 (4.0), CD27 (4.0), BTLA (3.9), PHEX (3.6), ICOS (3.4), CD7 (3.3), CD72 (3.2), SIRPG (3.1), CD2 (3.1), CD3G (3.0), HLA-DRA (3.0), SPIB (2.9), IL21R (2.8), FOS (2.8), CXCR3 (2.8), TRAT1 (2.8), SH2D1A (2.7), CD8B (2.6), CD45R0 (2.5), SOD2 (2.5), NFATC2 (2.2), DUSP2 (2.2), PSMB8 (2.1)). HSPA12B was downregulated in TCMR, compared to active ABMR (FC 2.2). Within the active ABMR group, there were no differences in gene expression profiles between C4d-positive and C4d-negative biopsies. Additionally, there were no statistically significant differences in gene expression between BKVN and TCMR.
*Conclusions: GEP assessed by Nanostring nCounter® platform (HistoMap, CareDx) can clearly differentiate between ABMR and TCMR. We did not identify significant differences between BKVN and TCMR, nor between C4d-positive and C4d-negative ABMR, which points towards similar pathophysiology in these two diagnoses.
To cite this abstract in AMA style:
Garg N, Degner K, Zhang H, Tian W, Aziz F, Parajuli S, Zhong W, Wilson N, Panzer S, Djamali A. Characterization of Kidney Allograft Pathology Using the Histomap Gene Expression Profile (GEP) and Formalin Fixed Paraffin Embedded (FFPE) Tissue [abstract]. Am J Transplant. 2022; 22 (suppl 3). https://atcmeetingabstracts.com/abstract/characterization-of-kidney-allograft-pathology-using-the-histomap-gene-expression-profile-gep-and-formalin-fixed-paraffin-embedded-ffpe-tissue/. Accessed May 16, 2025.« Back to 2022 American Transplant Congress