Dataset Information

High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq.

ABSTRACT: In this study, we extended co-indexing of transcriptomes and epitopes (CITE) to the spatial dimension and demonstrated high-plex protein and whole transcriptome co-mapping. We profiled 189 proteins and whole transcriptome in multiple mouse tissue types with spatial CITE sequencing and then further applied the method to measure 273 proteins and transcriptome in human tissues, revealing spatially distinct germinal center reactions in tonsil and early immune activation in skin at the Coronavirus Disease 2019 mRNA vaccine injection site.

SUBMITTER: Liu Y

PROVIDER: S-EPMC10567548 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq.

Liu Yang Y DiStasio Marcello M Su Graham G Asashima Hiromitsu H Enninful Archibald A Qin Xiaoyu X Deng Yanxiang Y Nam Jungmin J Gao Fu F Bordignon Pino P Cassano Marco M Tomayko Mary M Xu Mina M Halene Stephanie S Craft Joseph E JE Hafler David D Fan Rong R

Nature biotechnology 20230223 10

In this study, we extended co-indexing of transcriptomes and epitopes (CITE) to the spatial dimension and demonstrated high-plex protein and whole transcriptome co-mapping. We profiled 189 proteins and whole transcriptome in multiple mouse tissue types with spatial CITE sequencing and then further applied the method to measure 273 proteins and transcriptome in human tissues, revealing spatially distinct germinal center reactions in tonsil and early immune activation in skin at the Coronavirus Di ...[more]

PMID: 36823353

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Project description:Background Clinical guidelines recommend the use of established T2 mapping sequences to detect and quantify myocarditis and edema, but T2 mapping is performed in two dimensions with limited coverage and repetitive breath holds. Purpose To assess the reproducibility of an accelerated free-breathing three-dimensional (3D) whole-heart T2 MRI mapping sequence in phantoms and participants without a history of cardiac disease and to investigate its clinical performance in participants with suspected myocarditis. Materials and Methods Eight participants (three women, mean age, 31 years ± 4 [standard deviation]; cohort 1) without a history of cardiac disease and 25 participants (nine women, mean age, 45 years ± 17; cohort 2) with clinically suspected myocarditis underwent accelerated free-breathing 3D whole-heart T2 mapping with 100% respiratory scanning efficiency at 1.5 T. The participants were enrolled from November 2018 to August 2020. Three repeated scans were performed on 2 separate days in cohort 1. Segmental variations in T2 relaxation times of the left ventricular myocardium were assessed, and intrasession and intersession reproducibility were measured. In cohort 2, segmental myocardial T2 values, detection of focal inflammation, and map quality were compared with those obtained from clinical breath-hold two-dimensional (2D) T2 mapping. Statistical differences were assessed using the nonparametric Mann-Whitney and Kruskal-Wallis tests, whereas the paired Wilcoxon signed-rank test was used to assess subjective scores. Results Whole-heart T2 maps were acquired in a mean time of 6 minutes 53 seconds ± 1 minute 5 seconds at 1.5 mm3 resolution. Breath-hold 2D and free-breathing 3D T2 mapping had similar intrasession (mean T2 change of 3.2% and 2.3% for 2D and 3D, respectively) and intersession (4.8% and 4.9%, respectively) reproducibility. The two T2 mapping sequences showed similar map quality (P = .23, cohort 2). Abnormal myocardial segments were identified with confidence (score 3) in 14 of 25 participants (56%) with 3D T2 mapping and only in 10 of 25 participants (40%) with 2D T2 mapping. Conclusion High-spatial-resolution three-dimensional (3D) whole-heart T2 mapping shows high intrasession and intersession reproducibility and helps provide T2 myocardial characterization in agreement with clinical two-dimensional reference, while enabling 3D assessment of focal disease with higher confidence. © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Friedrich in this issue.

Dataset Information

High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq.

Publications

High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq.

Similar Datasets

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