Targeted therapy guided by single-cell transcriptomic analysis in drug-induced hypersensitivity syndrome: a case report

Kim, Doyoung; Kobayashi, Tetsuro; Voisin, Benjamin; Jo, Jay‐Hyun; Sakamoto, Keiko; Jin, Seon-Pil; Kelly, Michael C.; Pasieka, Helena B.; Naff, Jessica L.; Meyerle, Jon H; Ikpeama, Ijeoma; Fahle, Gary A.; Davis, Fred P.; Rosenzweig, Sergio D.; Alejo, Julie; Pittaluga, Stefania; Kong, Heidi H.; Freeman, Alexandra F.

doi:10.1038/s41591-019-0733-7

Cited by 140 publications

(112 citation statements)

References 39 publications

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“…The increased sensitivity of gene detection and transcript capture afforded by Seq-Well S 3 enhances the strength of the inferences and hypotheses that can be generated when examining the cellular and molecular features of disease pathophysiology by using scRNA-seq. To date, single-cell analyses of healthy and diseased human skin have revealed heterogeneity among immune and parenchymal cell types ( Cheng et al., 2018 ; He et al., 2020 ; Kim et al., 2020 ; Tabib et al., 2018 ). However, these studies have largely focused on a single cell type or disease.…”

Section: Discussionmentioning

confidence: 99%

Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies

et al. 2020

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Summary High-throughput single-cell RNA-sequencing (scRNA-seq) methodologies enable characterization of complex biological samples by increasing the number of cells that can be profiled contemporaneously. Nevertheless, these approaches recover less information per cell than low-throughput strategies. To accurately report the expression of key phenotypic features of cells, scRNA-seq platforms are needed that are both high fidelity and high throughput. To address this need, we created Seq-Well S 3 (“Second-Strand Synthesis”), a massively parallel scRNA-seq protocol that uses a randomly primed second-strand synthesis to recover complementary DNA (cDNA) molecules that were successfully reverse transcribed but to which a second oligonucleotide handle, necessary for subsequent whole transcriptome amplification, was not appended due to inefficient template switching. Seq-Well S 3 increased the efficiency of transcript capture and gene detection compared with that of previous iterations by up to 10- and 5-fold, respectively. We used Seq-Well S 3 to chart the transcriptional landscape of five human inflammatory skin diseases, thus providing a resource for the further study of human skin inflammation.

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Section: Discussionmentioning

confidence: 99%

Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies

et al. 2020

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“…GEO (https://www.ncbi.nlm.nih.gov/geo/) or Human Cell Atlas (https://www.humancellatlas.org). Totally, we curated single cell gene expression matrices of 13 human tissues, including lung [8], liver [9], ileum [10], rectum [10], blood [11], bone marrow [12], skin [13], spleen [14], esophagus [14], colon [15], eye [16], stomach [17] and kidney [18] (Table S1). For each tissue, we performed cell clustering and dimension reduction on the scaled gene expression matrix using Seurat package [19].…”

Section: Cell Type Identification In 13 Human Tissuesmentioning

confidence: 99%

Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses

Shen

Zhang

et al. 2020

Biochemical and Biophysical Research Communications

838

774

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a b s t r a c tThe new coronavirus (SARS-CoV-2) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by SARS-CoV-2 to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. SARS-CoV-2 may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell co-expression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins. Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted "CellPhoneDB" analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis.

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“…GEO (https://www.ncbi.nlm.nih.gov/geo/) or Human Cell Atlas (https://www.humancellatlas.org). Totally, we curated single cell gene expression matrices of 13 human tissues, including lung [11], liver [12], ileum [13], rectum [13], blood [14], bone marrow [15], skin [16], spleen [17], esophagus [17], colon [18], eye [19], stomach [20] and kidney [21] ( Table S1). The raw count matrix was normalized and scaled by Seurat package [22] (Materials and Methods).…”

Section: Cell Type Identification In 13 Human Tissuesmentioning

confidence: 99%

Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses

Shen

Zhang

et al. 2020

Preprint

158

166

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The new coronavirus (2019-nCoV) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by 2019-nCov to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. 2019-nCoV may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell coexpression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins.Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted "CellPhoneDB" analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis.

show abstract

Targeted therapy guided by single-cell transcriptomic analysis in drug-induced hypersensitivity syndrome: a case report

Cited by 140 publications

References 39 publications

Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies

Second-Strand Synthesis-Based Massively Parallel scRNA-Seq Reveals Cellular States and Molecular Features of Human Inflammatory Skin Pathologies

Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses

Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses

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