Recommendations for mRNA analysis of micro-dissected glomerular tufts from paraffin-embedded human kidney biopsy samples

Abstract

BackgroundGlomeruli are excellent pre-determined natural structures for laser micro-dissection. Compartment-specific glomerular gene expression analysis of formalin-fixed paraffin-embedded renal biopsies could improve research applications. The major challenge for such studies is to obtain good-quality RNA from small amounts of starting material, as applicable for the analysis of glomerular compartments. In this work, we provide data and recommendations for an optimized workflow of glomerular mRNA analysis.ResultsWith a proper resolution of the camera and screen provided by the next generation of micro-dissection systems, we are able to separate parietal epithelial cells from glomerular tufts. Selected compartment-specific transcripts (WT1 and GLEPP1 for glomerular tuft as well as PAX2 for parietal epithelial cells) seem to be reliable discriminators for these micro-dissected glomerular substructures. Using the phenol–chloroform extraction and hemalaun-stained sections (2 µm), high amounts of Bowman’s capsule transections (> 300) reveal sufficient RNA concentrations (> 300 ng mRNA) for further analysis. For comparison, in unstained sections from a number of 60 glomerular transections upwards, a minimum amount of 157 ng mRNA with a reasonable mRNA purity [A260/A280 ratio of 1.5 (1.4/1.7) median (25th/75th percentiles)] was reversely transcribed into cDNA. Comparing the effect of input RNA (20, 60, 150 and 300 micro-dissected glomerular transections), transcript expression of POLR2A significantly correlated when 60 and 150 laser micro-dissected glomerular transections were used for analysis. There was a lower inter-assay coefficient of variability for ADAMTS13, when at least 60 glomerular transections were used. According to the algorithms of geNormPlus and NormFinder, PGK1 and PPIA are more stable glomerular reference transcripts compared to GUSB, GAPDH, POLR2A, RPLPO, TBP, B2M, ACTB, 18SrRNA and HMBS.ConclusionsOur approach implements compartment-specific glomerular mRNA expression analysis into research applications, even regarding glomerular substructures like parietal epithelial cells. We recommend using of at least 60 micro-dissected unstained glomerular or 300 hemalaun-stained Bowman’s capsule transections to obtain sufficient input mRNA for reproducible results. Hereby, the range of RNA concentrations in 60 micro-dissected glomeruli is low and appropriate normalization of Cq values using our suggested reference transcripts (PGK1 and PPIA) allows compensation with respect to different amounts of RNA purity and quantity.Electronic supplementary materialThe online version of this article (10.1186/s12867-018-0103-x) contains supplementary material, which is available to authorized users.

Transcriptomic profiling of nuclei from PFA-fixed and FFPE brain tissues

“…Paraformaldehyde fixation (PFA) followed by paraffin embedding had been the preferred preservation method for tissue samples for decades since it maintains morphological features of the original tissue well 1,2 . FFPE tissues transcriptomic mainly focus on large sample RNA-seq analysis 3 and spatial transcriptome research based on micro-region (LCM, Pick-Seq) [4][5][6] or gene chip with spatial barcode (10x visium) 7 . Single-cell RNA sequencing (scRNA-seq) technology had emerged as the most powerful instrument for assessing cell-type heterogeneity 8 .…”

Selection of endogenous control genes for normalising gene expression data derived from formalin-fixed paraffin-embedded tumour tissue

“…To facilitate selection of control genes, TaqMan endogenous control array cards are available with 16 candidate genes. These genes have been used for normalization in human tissue gene expression studies including bladder 14 , thyroid 15 , hepatocellular 16 , breast 9 , gastric 17 , cervical 18 , endometrial 19 , non-small cell lung 20 , kidney 21 and prostate 22 cancer. Whilst bioinformatic interrogation of TCGA provides a useful verification of gene expression stability it is unsuitable for endogenous control gene selection for TaqMan Array cards as the TCGA database is derived using RNA sequencing.…”