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Abstract Number: 2950

10X Genomics-Based Single-Cell RNA-Seq Analysis Identifies a Transcriptional Landscape of Inflammation and Fibrosis in Lupus Nephritis​

Hemant Suryawanshi1, Evan Der2, Pavel Morozov1, Robert M. Clancy3, Beatrice Goilav4, H. Michael Belmont3, Peter M. Izmirly5, Nicole Bornkamp6, Nicole Jordan7, Ming Wu3, Judith A. James8, Joel M. Guthridge9, Soumya Raychaudhuri10, Jill P. Buyon3, Chaim Putterman2 and Thomas Tuschl1, 1Howard Hughes Medical Institute and The Rockefeller University, New York, NY, 2Albert Einstein College of Medicine, Bronx, NY, 3NYU School of Medicine, New York, NY, 4Division of Nephrology, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY, 5Rheumatology, NYU School of Medicine, New York, NY, 6Medicine, NYU School of Medicine, New York, NY, 7Division of Rheumatology, Albert Einstein College of Medicine, Bronx, NY, 8Oklahoma Medical Research Foundation, Oklahoma City, OK, 9Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, 10Harvard Medical School, Boston, MA

Meeting: 2018 ACR/ARHP Annual Meeting

Keywords: fibrosis, genomics and lupus nephritis, RNA

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Session Information

Date: Wednesday, October 24, 2018

Session Title: 6W024 ACR Abstract: SLE–Etiology & Pathogenesis II (2946–2951)

Session Type: ACR Concurrent Abstract Session

Session Time: 11:00AM-12:30PM

Background/Purpose: Renal histology remains a primary tool for classification and treatment decisions in lupus nephritis (LN). Single-cell RNA-seq (scRNA-seq) analysis may provide mechanistic insights into the genesis; more precisely categorize different pathologic subtypes; and better inform treatment decisions and prognosis. Here we characterized single-cell transcriptome profiles of the renal cellular landscape using scRNA-seq.

Methods: ScRNA-seq was performed on ~2 mg cryostored kidney tissue collected from clinically indicated renal biopsies in 9 SLE patients and 2 healthy transplant donors. A droplet-based 10X Chromium platform (10X Genomics) was used to capture single cells in emulsion followed by cDNA synthesis. The cDNA library was sequenced on Ilumina HiSeq 2500. Cell-barcode and unique molecular identifiers (UMIs) were tagged in read1, an adapter was trimmed from 5’ of read2 and poly(A) sequences of length 6 or more were removed. The resulting reads were aligned to the human (hg38) reference genome and a single cell gene expression matrix was generated. Using a graph-based method embedded in the Seurat package, cell clustering analysis was performed. Cells with > 25% mitochondrial content were considered poor quality and filtered out as were any cells with < 100 genes detected.

Results: We obtained 16,192 and 3,104 high-quality scRNA-seq profiles from 9 LN patients (class I, II, IV/V and IV) and 2 donor controls respectively. Graph-based clustering analysis revealed several cell clusters as visualized by t-distributed stochastic neighbor embedding (t-SNE). Differential gene expression analysis along with expression of established lineage markers revealed these clusters as loop of Henle (LH), proximal convoluted tubule (PCT), distal convoluted tubule (DCT), intercalated cells (IC), mesangial cells (MC), podocytes (PC), T cells (TC), macrophages (MAC), B cells (B cell), plasmablasts (PB), endothelial cells (EC) and fibroblasts (FB). Differential gene expression analysis revealed elevated levels of interferon response genes such as IFI6, IFITM1, IFITM3 and ISG15 in CD, DCT and EC of LN samples. In addition, WFDC2, recently described as an LN biomarker, was upregulated in CD and DCT of LN samples. PCT in the LN samples revealed increased expression of COL4A1, COL4A2 and COL18A1 genes whose proteins form the structural component of the basement membrane. FB detected in the LN samples expressed COL1A1, COL1A2, and COL3A1 as the most abundant collagen genes.

Conclusion: ScRNA-seq derived from excess and limited cryostored renal biopsy tissue in LN can be used to generate a cellular atlas invaluable to the study of heterogeneity in disease. These data provide important insights into potential pathogenic mechanisms, particularly with regard to tissue fibrosis so highly relevant to the ultimate renal prognosis.


Disclosure: H. Suryawanshi, None; E. Der, None; P. Morozov, None; R. M. Clancy, None; B. Goilav, None; H. M. Belmont, Exagen, 2; P. M. Izmirly, None; N. Bornkamp, None; N. Jordan, None; M. Wu, None; J. A. James, None; J. M. Guthridge, None; S. Raychaudhuri, None; J. P. Buyon, Exagen, 2; C. Putterman, None; T. Tuschl, None.

To cite this abstract in AMA style:

Suryawanshi H, Der E, Morozov P, Clancy RM, Goilav B, Belmont HM, Izmirly PM, Bornkamp N, Jordan N, Wu M, James JA, Guthridge JM, Raychaudhuri S, Buyon JP, Putterman C, Tuschl T. 10X Genomics-Based Single-Cell RNA-Seq Analysis Identifies a Transcriptional Landscape of Inflammation and Fibrosis in Lupus Nephritis​ [abstract]. Arthritis Rheumatol. 2018; 70 (suppl 10). https://acrabstracts.org/abstract/10x-genomics-based-single-cell-rna-seq-analysis-identifies-a-transcriptional-landscape-of-inflammation-and-fibrosis-in-lupus-nephritis%e2%80%8b/. Accessed January 23, 2021.
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