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 Single cell transcriptome atlas of mouse mammary epithelial cells across development

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Bhupinder Pal ◽  
Yunshun Chen ◽  
Michael J. G. Milevskiy ◽  
François Vaillant ◽  
Lexie Prokopuk ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Single Cell ◽  
Developmental Stages ◽  
Mammary Epithelial Cells ◽  
Expression Profiles ◽  
Single Cells ◽  
Chromatin Accessibility ◽  
Mammary Epithelial ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Abstract Background Heterogeneity within the mouse mammary epithelium and potential lineage relationships have been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary ontogeny, we profiled single cells from nine different developmental stages spanning late embryogenesis, early postnatal, prepuberty, adult, mid-pregnancy, late-pregnancy, and post-involution, as well as the transcriptomes of micro-dissected terminal end buds (TEBs) and subtending ducts during puberty. Methods The single cell transcriptomes of 132,599 mammary epithelial cells from 9 different developmental stages were determined on the 10x Genomics Chromium platform, and integrative analyses were performed to compare specific time points. Results The mammary rudiment at E18.5 closely aligned with the basal lineage, while prepubertal epithelial cells exhibited lineage segregation but to a less differentiated state than their adult counterparts. Comparison of micro-dissected TEBs versus ducts showed that luminal cells within TEBs harbored intermediate expression profiles. Ductal basal cells exhibited increased chromatin accessibility of luminal genes compared to their TEB counterparts suggesting that lineage-specific chromatin is established within the subtending ducts during puberty. An integrative analysis of five stages spanning the pregnancy cycle revealed distinct stage-specific profiles and the presence of cycling basal, mixed-lineage, and 'late' alveolar intermediates in pregnancy. Moreover, a number of intermediates were uncovered along the basal-luminal progenitor cell axis, suggesting a continuum of alveolar-restricted progenitor states. Conclusions This extended single cell transcriptome atlas of mouse mammary epithelial cells provides the most complete coverage for mammary epithelial cells during morphogenesis to date. Together with chromatin accessibility analysis of TEB structures, it represents a valuable framework for understanding developmental decisions within the mouse mammary gland.

scholarly journals Scirpy: A Scanpy extension for analyzing single-cell T-cell receptor sequencing data

2020 ◽  
Author(s):  
Gregor Sturm ◽  
Tamas Szabo ◽  
Georgios Fotakis ◽  
Marlene Haider ◽  
Dietmar Rieder ◽  
...  
Keyword(s):  
T Cell ◽  
Single Cell ◽  
Large Scale ◽  
Single Cells ◽  
Cell Receptor ◽  
Sequencing Data ◽  
Seamless Integration ◽  
T Cell Phenotypes ◽  
Cell Phenotypes

AbstractSummaryAdvances in single-cell technologies have enabled the investigation of T cell phenotypes and repertoires at unprecedented resolution and scale. Bioinformatic methods for the efficient analysis of these large-scale datasets are instrumental for advancing our understanding of adaptive immune responses in cancer, but also in infectious diseases like COVID-19. However, while well-established solutions are accessible for the processing of single-cell transcriptomes, no streamlined pipelines are available for the comprehensive characterization of T cell receptors. Here we propose Scirpy, a scalable Python toolkit that provides simplified access to the analysis and visualization of immune repertoires from single cells and seamless integration with transcriptomic data.Availability and implementationScirpy source code and documentation are available at https://github.com/icbi-lab/scirpy.

scholarly journals Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data

2020 ◽  
Vol 36 (18) ◽  
pp. 4817-4818 ◽  
Author(s):  
Gregor Sturm ◽  
Tamas Szabo ◽  
Georgios Fotakis ◽  
Marlene Haider ◽  
Dietmar Rieder ◽  
...  
Keyword(s):  
T Cell ◽  
Single Cell ◽  
Large Scale ◽  
Single Cells ◽  
Cell Receptor ◽  
Supplementary Information ◽  
Sequencing Data ◽  
Seamless Integration ◽  
T Cell Phenotypes ◽  
Cell Phenotypes

Abstract Summary Advances in single-cell technologies have enabled the investigation of T-cell phenotypes and repertoires at unprecedented resolution and scale. Bioinformatic methods for the efficient analysis of these large-scale datasets are instrumental for advancing our understanding of adaptive immune responses. However, while well-established solutions are accessible for the processing of single-cell transcriptomes, no streamlined pipelines are available for the comprehensive characterization of T-cell receptors. Here, we propose single-cell immune repertoires in Python (Scirpy), a scalable Python toolkit that provides simplified access to the analysis and visualization of immune repertoires from single cells and seamless integration with transcriptomic data. Availability and implementation Scirpy source code and documentation are available at https://github.com/icbi-lab/scirpy. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Lipidomics Revealed Aberrant Metabolism of Lipids Including FAHFAs in Renal Tissue in the Progression of Lupus Nephritis in a Murine Model

Metabolites ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 142
Author(s):  
Changfeng Hu ◽  
Yu Du ◽  
Xiaofen Xu ◽  
Haichang Li ◽  
Qiao Duan ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Fatty Acid ◽  
Lupus Nephritis ◽  
Lupus Erythematosus ◽  
Kidney Tissue ◽  
Renal Tissue ◽  
Autoimmune Response ◽  
Enzyme Linked Immunosorbent Assay ◽  
Shotgun Lipidomics ◽  
Necrosis Factor Alpha

Lupus nephritis (LN) is an inflammatory renal disease of patients with systemic lupus erythematosus with lots of immune complexes deposited in kidneys. Accumulated studies have demonstrated the close relationships among dyslipidaemia, inflammation, and autoimmune response, and oxidative stress in the patients. Lipids play numerous important roles in biological process and cellular functions. Herein, shotgun lipidomics was employed to quantitatively analyze cellular lipidomes in the renal tissue of MRL/lpr mice in the progression of LN (including pre-LN and LN state) with/without treated with glucocorticoids (GCs). The levels of cytokines (i.e., TNF-α (Tumor necrosis factor alpha) and IL-6 (Interleukin 6)) in the serum were measured by ELISA (enzyme-linked immunosorbent assay) kits. Renal histopathological changes and C3 deposition in the glomeruli of the mice were also determined. Lipidomics analysis revealed that the ectopic fat deposition and the aberrant metabolism of lipids that were relevant to oxidative stress (e.g., 4-hydroxyalkenal, ceramide, lysophospholipid species, etc.) always existed in the development of LN. Moreover, the anti-inflammatory FAHFA (fatty acid ester of hydroxyl fatty acid) species in the kidney tissue could largely reflect the severity of LN. Thus, they were a potential early biomarker for LN. In addition, the study also revealed that treatment with GCs could prevent the progression of LN, but greatly aggravate the aberrant metabolism of the lipids, particularly when used for a long time.

scholarly journals Comparative proteome signatures of trace samples by multiplexed Data-Independent Acquisition

2021 ◽  
Author(s):  
Claudia Ctortecka ◽  
Gabriela Krššáková ◽  
Karel Stejskal ◽  
Josef M. Penninger ◽  
Sasha Mendjan ◽  
...  
Keyword(s):  
Data Analysis ◽  
Protein Expression ◽  
Single Cell ◽  
Missing Values ◽  
Expression Profiles ◽  
Single Cells ◽  
Proteomics Data ◽  
Biological Origin ◽  
Low Input ◽  
Data Independent Acquisition

AbstractSingle cell transcriptomics has revolutionized our understanding of basic biology and disease. Since transcript levels often do not correlate with protein expression, it is crucial to complement transcriptomics approaches with proteome analyses at single cell resolution. Despite continuous technological improvements in sensitivity, mass spectrometry-based single cell proteomics ultimately faces the challenge of reproducibly comparing the protein expression profiles of thousands of individual cells. Here, we combine two hitherto opposing analytical strategies, DIA and Tandem-Mass-Tag (TMT)-multiplexing, to generate highly reproducible, quantitative proteome signatures from ultra-low input samples. While conventional, data-dependent shotgun proteomics (DDA) of ultra-low input samples critically suffers from the accumulation of missing values with increasing sample-cohort size, data-independent acquisition (DIA) strategies do usually not take full advantage of isotope-encoded sample multiplexing. We developed a novel, identification-independent proteomics data-analysis pipeline that allows to quantitatively compare DIA-TMT proteome signatures across hundreds of samples independent of their biological origin, and to identify cell types and single protein knockouts. We validate our approach using integrative data analysis of different human cell lines and standard database searches for knockouts of defined proteins. These data establish a novel and reproducible approach to markedly expand the numbers of proteins one detects from ultra-low input samples, such as single cells.

scholarly journals Kidney tissue hypoxia dictates T cell–mediated injury in murine lupus nephritis

2020 ◽  
Vol 12 (538) ◽  
pp. eaay1620 ◽  
Author(s):  
Ping-Min Chen ◽  
Parker C. Wilson ◽  
Justin A. Shyer ◽  
Margaret Veselits ◽  
Holly R. Steach ◽  
...  
Keyword(s):  
T Cells ◽  
Lupus Nephritis ◽  
Lupus Erythematosus ◽  
Hypoxia Inducible Factor ◽  
Kidney Tissue ◽  
Renal Tissue ◽  
Tissue Hypoxia ◽  
Mouse Tissue ◽  
Low Oxygen ◽  
Environmental Adaptations

The kidney is a frequent target of autoimmune injury, including in systemic lupus erythematosus; however, how immune cells adapt to kidney’s unique environment and contribute to tissue damage is unknown. We found that renal tissue, which normally has low oxygen tension, becomes more hypoxic in lupus nephritis. In the injured mouse tissue, renal-infiltrating CD4+ and CD8+ T cells express hypoxia-inducible factor–1 (HIF-1), which alters their cellular metabolism and prevents their apoptosis in hypoxia. HIF-1–dependent gene-regulated pathways were also up-regulated in renal-infiltrating T cells in human lupus nephritis. Perturbation of these environmental adaptations by selective HIF-1 blockade inhibited infiltrating T cells and reversed tissue hypoxia and injury in murine models of lupus. The results suggest that targeting HIF-1 might be effective for treating renal injury in autoimmune diseases.

scholarly journals Single-cell entropy for accurate estimation of differentiation potency from a cell’s transcriptome

2016 ◽  
Author(s):  
Andrew E Teschendorff
Keyword(s):  
Stem Cell ◽  
Cancer Stem Cell ◽  
Single Cell ◽  
Time Course ◽  
Single Cells ◽  
Interaction Network ◽  
Cellular Interaction ◽  
Accurate Estimation ◽  
Differentiation Potential ◽  
Cell Phenotypes

AbstractThe ability to quantify differentiation potential of single cells is a task of critical importance for single-cell studies. So far however, there is no robust general molecular correlate of differentiation potential at the single cell level. Here we show that differentiation potency of a single cell can be approximated by computing the signaling promiscuity, or entropy, of a cell’s transcriptomic profile in the context of a cellular interaction network, without the need for model training or feature selection. We validate signaling entropy in over 7,000 single cell RNA-Seq profiles, representing all main differentiation stages, including time-course data. We develop a novel algorithm called Single Cell Entropy (SCENT), which correctly identifies known cell subpopulations of varying potency, enabling reconstruction of cell-lineage trajectories. By comparing bulk to single cell data, SCENT reveals that expression heterogeneity within single cell populations is regulated, pointing towards the importance of cell-cell interactions. In the context of cancer, SCENT can identify drug resistant cancer stem-cell phenotypes, including those obtained from circulating tumor cells. In summary, SCENT can directly estimate the differentiation potency and plasticity of single-cells, allowing unbiased quantification of intercellular heterogeneity, and providing a means to identify normal and cancer stem cell phenotypes.Software AvailabilitySCENT is freely available as an R-package from github: https://github.com/aet21/SCENT

scholarly journals Rapid microfluidic isolation of virally infected primary bronchial epithelial cells for single-cell RNA sequencing

BioTechniques ◽  
2021 ◽  
Vol 71 (1) ◽  
pp. 387-391
Author(s):  
Lucy M Kimbley ◽  
Rachel Parker ◽  
Maaike Sybil Jongen ◽  
John W Holloway ◽  
Emily J Swindle ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Single Cells ◽  
Bronchial Epithelial Cells ◽  
Cdna Libraries ◽  
Bronchial Epithelial ◽  
Rna Integrity ◽  
Single Cell Rna Sequencing ◽  
Primary Bronchial Epithelial Cells

Single-cell RNA sequencing (scRNA-seq) of the bronchial epithelium enables examination of cellular subtypes and their responses to viral infections. Here, an optimized method for the isolation of virally infected primary bronchial epithelial cells using a commercially available microfluidic device is presented. Using this method single cells can be rapidly isolated with minimal equipment available in most laboratories. Isolation can be carried out inside biological safety cabinets, permitting the use of virally infected cells. Both cell-line and primary cells isolated using the device retained sufficient RNA integrity for the generation of short-read sequencing-compatible cDNA libraries to facilitate scRNA-seq.

Correlation Between Serological Makers and Immunofluorescence Deposits i n Kidney Tissue of Patients with Lupus Nephritis

2019 ◽  
Vol 9 (02) ◽  
Author(s):  
Haider S Al-Hadad ◽  
Aqeel Abbas Matrood ◽  
Maha Abdalrasool Almukhtar ◽  
Haider Jabur Kehiosh ◽  
Riyadh Muhi Al-Saegh
Keyword(s):  
Lupus Nephritis ◽  
Lupus Erythematosus ◽  
Kidney Biopsy ◽  
Pearson Correlation ◽  
Standard Procedure ◽  
Kidney Tissue ◽  
P Value ◽  
American College Of Rheumatology ◽  
Immune Deposits ◽  
Number Of Patients

Background: Systemic lupus erythematosus (SLE) is an autoimmune disease. Few biomarkers for SLE have been validated and widely accepted for the laboratory follow-up of inflammatory activity. In SLE patients, with lupus nephritis (LN), complement activation leads to fluctuation of serum C3 and C4 that are frequently used as clinicalm biomarker of disease activity in SLE. Patients and Methods: In this study the number of patients were 37, seven patients were excluded for incomplete data collection, 28 were females ,2 were males. The duration of the study is two years from 2015 to 2017. Patients were considered to have SLE and LN according to American College of Rheumatology (ACR) criteria, and International Society of Nephrology/ Renal Pathology Society (ISN/RPS). All patients were evaluated withm clinical presentation, laboratory investigations. Our patients underwent kidney biopsy according to standard procedure by Kerstin Amann, and their tissue specimens were studied in the laboratory with light microscope (LM) and immunofluorescence microscope reagents. The relationship between the serological markers and immunofluorescence deposits in kidney biopsy of all patients were studied using the statistical analysis of Pearson correlation and single table student's T test. A P value 0.05 was considered statistically significant. Results: The granular pattern of IF deposits was present in all LN patients, and in more than two third of patients these IF deposits presented in glomerular, tubular, and mesangium sites. While less than one third of patients had IF deposits in the mesangium only. There was no statistically significant correlation between serum ANA, anti-dsDNA, and IF deposits of different types. There was significant correlation between serum C3 and C4 hypocomplementemia and IgG immune deposits in kidney biopsy, and there was significant relationship between serum C3 hypocomplementemia and full house immunofluorescence (FHIF) deposits inm kidney biopsy.Conclusions:Immunofluorescence deposits is mainly granular pattern in LN patients. There was no significant association between serum ANA, anti-dsDNA, and immune deposits in kidney tissue. Immunofluorescence deposits of IgG type correlates significantly with serum C3 and C4 hypocomplemetemia, and these immune deposits in association with low complement levels correlates with LN flare. There was significant correlation between C3 hypocomplementemia and FHIF.

In-Situ Dual Beam (FIBSEM) Techniques for Probe Pad Deposition and Dielectric Integrity Inspection in 0.2 μm Technology DRAM Single Cells

1999 ◽  
Author(s):  
Gunnar Zimmermann ◽  
Richard Chapman
Keyword(s):  
Electron Beam ◽  
Single Cell ◽  
Single Cells ◽  
Ion Beam ◽  
Gate Oxide ◽  
Ion Milling ◽  
Dual Beam ◽  
Sem Imaging ◽  
Innovative Techniques

Abstract Dual beam FIBSEM systems invite the use of innovative techniques to localize IC fails both electrically and physically. For electrical localization, we present a quick and reliable in-situ FIBSEM technique to deposit probe pads with very low parasitic leakage (Ipara < 4E-11A at 3V). The probe pads were Pt, deposited with ion beam assistance, on top of highly insulating SiOx, deposited with electron beam assistance. The buried plate (n-Band), p-well, wordline and bitline of a failing and a good 0.2 μm technology DRAM single cell were contacted. Both cells shared the same wordline for direct comparison of cell characteristics. Through this technique we electrically isolated the fail to a single cell by detecting leakage between the polysilicon wordline gate and the cell diffusion. For physical localization, we present a completely in-situ FIBSEM technique that combines ion milling, XeF2 staining and SEM imaging. With this technique, the electrically isolated fail was found to be a hole in the gate oxide at the bad cell.

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