Kidney Week

Abstract: TH-PO033

RNA-Seq Profiling of Microdissected Glomeruli in Clinically Early IgA Nephropathy

Session Information

• Glomerular: Basic/Experimental Immunology and Inflammation - I
  November 02, 2017 | Location: Hall H, Morial Convention Center
  Abstract Time: 10:00 AM - 10:00 AM

Category: Glomerular

• 1001 Glomerular: Basic/Experimental Immunology and Inflammation

Authors

• Park, Sehoon, Seoul National University Hospital, Jongno-gu, SEOUL, Korea (the Republic of)

Sehoon Park,

• Lee, Jae Wook, National Cancer Center, Seoul, Korea (the Republic of)

Jae Wook Lee,

• Yang, Seung Hee, Seoul National University Hospital, Jongno-gu, SEOUL, Korea (the Republic of)

Seung Hee Yang,

• Kim, Dong Ki, Seoul National University Hospital, Jongno-gu, SEOUL, Korea (the Republic of)

Dong Ki Kim,

• Kim, Yon Su, Seoul National University Hospital, Jongno-gu, SEOUL, Korea (the Republic of)

Yon Su Kim,

• Lee, Hajeong, Seoul National University Hospital, Jongno-gu, SEOUL, Korea (the Republic of)

Hajeong Lee,

Background

IgA nephropathy (IgAN) is the most common primary glomerular disease worldwide and also a leading cause of chronic kidney disease and renal failure. Although recent studies have shed light on genetic variants associated with IgAN, transcriptomic changes in the glomerulus and their relevance to the pathophysiology of IgAN have been poorly defined. To identify early gene-expression changes in IgAN, we profiled the transcriptome in microdissected human glomeruli using deep sequencing of RNA species (RNA-seq).

Methods

Glomeruli were microdissected from the biopsy specimen obtained from 6 IgAN patients with preserved renal function (eGFR > 60 mL/min/1.73m² and proteinuria < 1 g/d). As negative controls, normal glomeruli were obtained from patients undergoing nephrectomy (n=3). Glomerular mRNAs were captured using oligo-dT primers and made into cDNA libraries for Illumina sequencing. After mapping to the human reference genome (GRCh38 primary assembly), reads mapping to Ensembl genes were counted. Wald test for a negative binomial model was used to call differentially expressed genes.

Results

Each library produced 29-43 million pairs of reads, more than 70% of which were uniquely aligned to the human genome. Of 17,833 Ensembl genes with >10 reads, 285 were upregulated and 434 downregulated in the IgAN glomeruli. Downregulated genes included transcription factors (FOS, FOSB, ZFP36, EGR1, ATF3, JUNB, NR4A2, JUN, SKI, POU5F1, KLF9, KLF8, KLF4, KLF2, CTNNB1, DMTF1, and CREBBP), periostin (POSTN), cytoskeletal proteins (MYO15A and TPM2), and C-X-C motif chemokine ligand 2 (CXCL2). Among upregulated genes were integrin subunits (ITGAV, ITGA4, and ITGB3), histone deacetylase (HDAC5), adenylate cyclase 7 (ADCY7), cyclin D2 (CCND2), homeobox D1 (HOXD1), and interleukin-6 receptor (IL6R). None of the genes positively reported in the GWAS studies on IgAN have been found to be differentially expressed in our dataset.

Conclusion

In human glomeruli obtained from patients with clinically early IgAN, RNA-seq revealed altered expression of DNA-binding transcription factors, cytoskeletal proteins, and integrin subunits that are potentially important for maintaining the integrity of the glomerular filtration barrier.