Urine Proteomics and Renal Single Cell Transcriptomics Implicate IL ‐16 in Lupus Nephritis

2021 ◽  
Author(s):  
Andrea Fava ◽  
Deepak A. Rao ◽  
Chandra Mohan ◽  
Ting Zhang ◽  
Avi Rosenberg ◽  
...  
Keyword(s):  
Lupus Nephritis ◽  
Single Cell ◽  
Urine Proteomics

scholarly journals Integration of urine proteomics and renal single-cell genomics identifies an interferon-gamma response gradient in lupus nephritis

2020 ◽  
Author(s):  
Andrea Fava ◽  
Jill Buyon ◽  
Chandra Mohan ◽  
Ting Zhang ◽  
H. Michael Belmont ◽  
...  
Keyword(s):  
Lupus Nephritis ◽  
Single Cell ◽  
Interferon Gamma ◽  
Lupus Erythematosus ◽  
Patient Specific ◽  
Molecular Heterogeneity ◽  
Protein Biomarkers ◽  
Cd8 Cells ◽  
Urine Proteomics ◽  
Chemokine Gradient

AbstractLupus nephritis, one of the most serious manifestations of systemic lupus erythematosus (SLE), has both a heterogeneous clinical and pathological presentation. For example, proliferative nephritis identifies a more aggressive disease class that requires immunosuppression. However, the current classification system relies on the static appearance of histopathological morphology which does not capture differences in the inflammatory response. Therefore, a biomarker grounded in the disease biology is needed to understand the molecular heterogeneity of lupus nephritis and identify immunologic mechanism and pathways. Here, we analyzed the patterns of 1000 urine protein biomarkers in 30 patients with active lupus nephritis. We found that patients stratify over a chemokine gradient inducible by interferon-gamma. Higher values identified patients with proliferative lupus nephritis. After integrating the urine proteomics with the single-cell transcriptomics of kidney biopsies, it was observed that the urinary chemokines defining the gradient were predominantly produced by infiltrating CD8 T cells, along with natural killer and myeloid cells. The urine chemokine gradient significantly correlated with the number of kidney-infiltrating CD8 cells. These findings suggest that urine proteomics can capture the complex biology of the kidney in lupus nephritis. Patient-specific pathways may be noninvasively tracked in the urine in real time, enabling diagnosis and personalized treatment.

scholarly journals Integrated urine proteomics and renal single-cell genomics identify an IFN-γ response gradient in lupus nephritis

JCI Insight ◽  
2020 ◽  
Vol 5 (12) ◽  
Author(s):  
Andrea Fava ◽  
Jill Buyon ◽  
Chandra Mohan ◽  
Ting Zhang ◽  
H. Michael Belmont ◽  
...  
Keyword(s):  
Lupus Nephritis ◽  
Single Cell ◽  
Single Cell Genomics ◽  
Urine Proteomics ◽  
Ifn Γ ◽  
Response Gradient

scholarly journals 300 Insights from single-cell RNA sequencing of skin and kidney in lupus nephritis

2019 ◽  
Author(s):  
Evan Der ◽  
Hemant Suryawanshi ◽  
Pavel Morozov ◽  
Manjunath Kustagi ◽  
Beatrice Goilav ◽  
...  
Keyword(s):  
Lupus Nephritis ◽  
Single Cell ◽  
Rna Sequencing ◽  
Single Cell Rna Sequencing

scholarly journals Quantitative planar array screen of 1000 proteins uncovers novel urinary protein biomarkers of lupus nephritis

2020 ◽  
Vol 79 (10) ◽  
pp. 1349-1361
Author(s):  
Kamala Vanarsa ◽  
Sanam Soomro ◽  
Ting Zhang ◽  
Briony Strachan ◽  
Claudia Pedroza ◽  
...  
Keyword(s):  
Growth Factor ◽  
Lupus Nephritis ◽  
Disease Activity ◽  
Single Cell ◽  
Rna Sequencing ◽  
Lupus Erythematosus ◽  
Transforming Growth Factor ◽  
Sequencing Analysis ◽  
Potential Biomarker ◽  
Planar Array

ObjectiveThe goal of these studies is to discover novel urinary biomarkers of lupus nephritis (LN).MethodsUrine from systemic lupus erythematosus (SLE) patients was interrogated for 1000 proteins using a novel, quantitative planar protein microarray. Hits were validated in an independent SLE cohort with inactive, active non-renal (ANR) and active renal (AR) patients, in a cohort with concurrent renal biopsies, and in a longitudinal cohort. Single-cell renal RNA sequencing data from LN kidneys were examined to deduce the cellular origin of each biomarker.ResultsScreening of 1000 proteins revealed 64 proteins to be significantly elevated in SLE urine, of which 17 were ELISA validated in independent cohorts. Urine Angptl4 (area under the curve (AUC)=0.96), L-selectin (AUC=0.86), TPP1 (AUC=0.84), transforming growth factor-β1 (TGFβ1) (AUC=0.78), thrombospondin-1 (AUC=0.73), FOLR2 (AUC=0.72), platelet-derived growth factor receptor-β (AUC=0.67) and PRX2 (AUC=0.65) distinguished AR from ANR SLE, outperforming anti-dsDNA, C3 and C4, in terms of specificity, sensitivity and positive predictive value. In multivariate regression analysis, urine Angptl4, L-selectin, TPP1 and TGFβ1 were highly associated with disease activity, even after correction for demographic variables. In SLE patients with serial follow-up, urine L-selectin (followed by urine Angptl4 and TGFβ1) were best at tracking concurrent or pending disease flares. Importantly, several proteins elevated in LN urine were also expressed within the kidneys in LN, either within resident renal cells or infiltrating immune cells, based on single-cell RNA sequencing analysis.ConclusionUnbiased planar array screening of 1000 proteins has led to the discovery of urine Angptl4, L-selectin and TGFβ1 as potential biomarker candidates for tracking disease activity in LN.

scholarly journals A protocol for single-cell transcriptomics from cryopreserved renal tissue and urine for the Accelerating Medicine Partnership (AMP) RA/SLE network

2018 ◽  
Author(s):  
Deepak A. Rao ◽  
Celine C. Berthier ◽  
Arnon Arazi ◽  
Anne Davidson ◽  
Yanyan Liu ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Lupus Nephritis ◽  
Single Cell ◽  
Single Cells ◽  
Kidney Tissue ◽  
Enzymatic Digestion ◽  
Renal Tissue ◽  
Low Input ◽  
Intact Kidney ◽  
Cell Phenotypes

ABSTRACTOBJECTIVEThere is a critical need to define the cells that mediate tissue damage in lupus nephritis. Here we aimed to establish a protocol to preserve lupus nephritis kidney biopsies and urine cell samples obtained at multiple clinical sites for subsequent isolation and transcriptomic analysis of single cells.METHODSFresh and cryopreserved kidney tissue from tumor nephrectomies and lupus nephritis kidney biopsies were disaggregated by enzymatic digestion. Cell yields and cell composition were assessed by flow cytometry. Transcriptomes of leukocytes and epithelial cells were evaluated by low-input and single cell RNA-seq.RESULTSCryopreserved kidney tissue from tumor nephrectomies and lupus nephritis biopsies can be thawed and dissociated to yield intact, viable leukocytes and epithelial cells. Cryopreservation of intact kidney tissue provides higher epithelial cell yields compared to cryopreservation of single cell suspensions from dissociated kidneys. Cell yields and flow cytometric cell phenotypes are comparable between cryopreserved kidney samples and paired kidney samples shipped overnight on wet ice. High-quality single cell and low-input transcriptomic data were generated from leukocytes from both cryopreserved lupus nephritis kidney biopsies and urine, as well as from a subset of kidney epithelial cells.CONCLUSIONThe AMP RA/SLE cryopreserved tissue analysis pipeline provides a method for centralized processing of lupus nephritis kidney biopsies and urine samples to generate robust transcriptomic analyses in multi-center studies.

scholarly journals Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways

2019 ◽  
Vol 20 (7) ◽  
pp. 915-927 ◽  
Author(s):  
Evan Der ◽  
◽  
Hemant Suryawanshi ◽  
Pavel Morozov ◽  
Manjunath Kustagi ◽  
...  
Keyword(s):  
Lupus Nephritis ◽  
Single Cell ◽  
Tubular Cell ◽  
Type I ◽  
Type I Ifn
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