In-Situ Tissue-Based Gene Expression Profiling is a Reliable Method to Detect Gene Transcripts in Human Kidney Transplant Biopsies

D. Dobi,¹ J. Henrik,² T. Sigdel,² A. Chen,¹ Z. Laszik.¹

¹Department of Pathology, University of California, San Francisco, San Francisco, CA
²Department of Surgery, University of California, San Francisco, San Francisco, CA.

Meeting: 2018 American Transplant Congress

Abstract number: A8

Keywords: Gene expression, Image analysis, Kidney transplantation

Session Information

Session Name: Poster Session A: Biomarkers, Immune Monitoring and Outcomes

Session Type: Poster Session

Date: Saturday, June 2, 2018

Session Time: 5:30pm-7:30pm

Presentation Time: 5:30pm-7:30pm

Location: Hall 4EF

Purpose. Validation studies that would enable the clinical application of quantitative in situ tissue-based gene expression profiling in renal transplantation are lacking. In this study, we validated an in situ hybridization (ISH) assay coupled with whole slide scanning and digital image analysis against a commercial gene-expression platform and assessed its reproducibility in a pilot set of renal transplant patients.

Methods. Gene expression analysis (GEA) and RNAscope ISH (ACDBio) were performed on formalin-fixed paraffin-embedded (FFPE) biopsies with normal morphology (n=4), with borderline changes (n=6), and with acute cellular rejection (ACR) (n=4). For GEA, nanoString nCounter Sprint platform was used with a customized panel of 30 genes relevant in ACR. CXCL-9, -10, and LCK ISH was performed with a chromogenic detection method followed by whole-slide digital image analysis. In two additional cases with ACR, 5-5 consecutive FFPE sections were evaluated for CXCL-9 expression with both chromogenic, and fluorescent ISH. Spearman's rank correlation, Pearson's correlation and intraclass correlation coefficient (ICC) were used where applicable.

Results. There was a strong correlation between the log2 transformed gene count measured by GEA and ISH spot count/1000 cells for CXCL-9 (Spearman's rho = 0.899), CXCL-10 (r = 0.841), and LCK (r=0.772), p < 0.001 for all tests. Both the chromogenic and the fluorescent detection method for ISH showed excellent ICC (0.994, 95 % CI 0.950 to 1.000, p<0.0005; and 0.970, 95 % CI 0.639 to 1.000, p=0.004, respectively).

Conclusion. ISH coupled with whole slide digital image analysis is comparable to nanoString nCounter Sprint platform in measuring the expression level of a selected set of genes relevant in ACR and is a highly reproducible assay. Therefore, it is feasible to be further tested in a larger scale clinical study.

CITATION INFORMATION: Dobi D., Henrik J., Sigdel T., Chen A., Laszik Z. In-Situ Tissue-Based Gene Expression Profiling is a Reliable Method to Detect Gene Transcripts in Human Kidney Transplant Biopsies Am J Transplant. 2017;17 (suppl 3).

To cite this abstract in AMA style:

Dobi D, Henrik J, Sigdel T, Chen A, Laszik Z. In-Situ Tissue-Based Gene Expression Profiling is a Reliable Method to Detect Gene Transcripts in Human Kidney Transplant Biopsies [abstract]. https://atcmeetingabstracts.com/abstract/in-situ-tissue-based-gene-expression-profiling-is-a-reliable-method-to-detect-gene-transcripts-in-human-kidney-transplant-biopsies/. Accessed May 16, 2025.

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