Dataset Information

Improved integration of single-cell transcriptome and surface protein expression by LinQ-View.

ABSTRACT: Multimodal advances in single-cell sequencing have enabled the simultaneous quantification of cell surface protein expression alongside unbiased transcriptional profiling. Here, we present LinQ-View, a toolkit designed for multimodal single-cell data visualization and analysis. LinQ-View integrates transcriptional and cell surface protein expression profiling data to reveal more accurate cell heterogeneity and proposes a quantitative metric for cluster purity assessment. Through comparison with existing multimodal methods on multiple public CITE-seq datasets, we demonstrate that LinQ-View efficiently generates accurate cell clusters, especially in CITE-seq data with routine numbers of surface protein features, by preventing variations in a single surface protein feature from affecting results. Finally, we utilized this method to integrate single-cell transcriptional and protein expression data from SARS-CoV-2-infected patients, revealing antigen-specific B cell subsets after infection. Our results suggest LinQ-View could be helpful for multimodal analysis and purity assessment of CITE-seq datasets that target specific cell populations (e.g., B cells).

SUBMITTER: Li L

PROVIDER: S-EPMC9017149 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature

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Improved integration of single-cell transcriptome and surface protein expression by LinQ-View.

Li Lei L Dugan Haley L HL Stamper Christopher T CT Lan Linda Yu-Ling LY Asby Nicholas W NW Knight Matthew M Stovicek Olivia O Zheng Nai-Ying NY Madariaga Maria Lucia ML Shanmugarajah Kumaran K Jansen Maud O MO Changrob Siriruk S Utset Henry A HA Henry Carole C Nelson Christopher C Jedrzejczak Robert P RP Fremont Daved H DH Joachimiak Andrzej A Krammer Florian F Huang Jun J Khan Aly A AA Wilson Patrick C PC

Cell reports methods 20210723 4

Multimodal advances in single-cell sequencing have enabled the simultaneous quantification of cell surface protein expression alongside unbiased transcriptional profiling. Here, we present LinQ-View, a toolkit designed for multimodal single-cell data visualization and analysis. LinQ-View integrates transcriptional and cell surface protein expression profiling data to reveal more accurate cell heterogeneity and proposes a quantitative metric for cluster purity assessment. Through comparison with ...[more]

PMID: 35475142

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Project description:Choline is used to synthesize phospholipids and a lack of choline induces a number of liver‑related diseases, including non‑alcoholic steatohepatitis. The current study characterized the choline uptake system, at molecular and functional levels, in the immortalized human hepatic cell line, Fa2N‑4, to identify the specific choline transporter involved in choline uptake. The present study also assesed whether choline deficiency or the inhibited choline uptake affected cell viability and apoptosis. Reverse transcription‑quantitative polymerase chain reaction (PCR) revealed choline transporter‑like protein 1 (CTL1) and CTL2 mRNA and protein expression in Fa2N‑4 cells. [Methyl‑3H]choline studies revealed choline uptake was saturable and mediated by a single transport system that functioned in a Na+‑independent but pH‑dependent manner, which was similar to CTL1. Hemicholinium‑3 (HC‑3), which is a choline uptake inhibitor, and choline deficiency inhibited cell viability, increased caspase‑3 and ‑7 activities, and increased fluorescein isothiocyanate‑Annexin V immunofluorescent staining indicated apoptosis. Immunofluorescent staining also revealed CTL1 and CTL2 localized in plasma and mitochondrial membranes, respectively. [Methyl‑3H]choline uptake was enhanced by a protein kinase C (PKC) activator, phorbol‑12‑myristate 13‑acetate (PMA). Immunofluorescence staining and western blot analysis demonstrated increased CTL1 expression on the cell membrane following PMA treatment. The results of current study indicated that extracellular choline is primarily transported via CTL1, relying on a direct H+ gradient that functions as a driving force in Fa2N‑4 cells. Furthermore, it was hypothesized that CTL1 and the choline uptake system are strongly associated with cell survival, and that the choline uptake system is modulated by PKC signaling via increased CTL1 expression on the cell surface. These findings provide further insights into the pathogenesis of liver disease involving choline metabolism.

Dataset Information

Improved integration of single-cell transcriptome and surface protein expression by LinQ-View.

Publications

Improved integration of single-cell transcriptome and surface protein expression by LinQ-View.

Similar Datasets

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