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May Literature Blitz
Time:2022-06-02 20:05:19  

 

May Top 10 Publications - Advances in Single Cell Sequencing

 

 

 

Our monthly single cell Literature Blitz column is back again. May featured a diverse collection of exciting new studies that advanced our understanding of single cell methods and disease treatments. Here is our selection of top publications featuring new advances and applications of single cell sequencing in pulmonary diseases, renal fibrosis, sepsis, meningioma, lymphoma, liver failure and hepatocarcinoma, COVID-19 and creation of a human cell atlas.

 

What are your May top choices?

Let us know in the comments.

 

[1] Lung Tissue RNA Profiling in Pulmonary Disease

[2] Renal Fibrosis and Chronic Kidney Disease

[3] Sepsis: Ulinstatin Treatment

[4] Profiling The Human Dura and Meningioma

[5] HDAC Inhibitor Therapy in B-cell Lymphoma

[6] The Tabula Sapiens – Human Single Cell Atlas

[7] Liver and HBV

[8] Human Placenta Mesenchymal Stem Cells

[9] Hepatocellular Carcinoma

[10] SARSCoV-2 in Monkey Lung vs Intestines

 

Lung Tissue RNA Profiling in Pulmonary Disease [↑]

 

 

[1] Sauler et al. Characterization of the COPD alveolar niche using single-cell RNA sequencing. Nat. Commun., 2022. [PubMed]

 

Chronic Obstructive Pulmonary Disease (COPD) is characterized by persistent inflammation and parenchymal lung tissue destruction, commonly caused by aerosolized pollutants, such as cigarette smoke (CS). The pathogenic cascade of COPD is initiated by repetitive insults to epithelial and endothelial cells within the distal airways and alveolar niche. Detailed knowledge of cell-type-specific mechanisms and the complex interactions among multiple lung cell types in COPD is lacking.

 

Sauler et al. sought to use single cell RNA sequencing to elucidate cell-specific transcriptional profiles of alveolar niche cells in COPD and better understand the pathobiology of this disease. They focused their analysis on three cell types commonly implicated in COPD pathogenesis: epithelial cells, endothelial cells, and alveolar macrophages, and identified a subpopulation of HHIP-expressing alveolar epithelial type II (AT2) cells that mediate COPD heritability and have aberrant expression of metabolic, antioxidant, and cellular stress response genes in COPD, including reduced expression of the cellular stress response gene NUPR1. Also, they identified a subpopulation of high metallothionein-expressing alveolar macrophages in the COPD lung.

 

 

 

 

Figure 1: UMAP plots of 111,540 single cells (Left) grouped into 37 distinct cell types (Right) with identification of COPD and control cells.

 

 

 

Renal Fibrosis and Chronic Kidney Disease [↑]

 

 

[2] Doke et al. Single-cell analysis identified the interaction of altered renal tubules with basophils orchestrating kidney fibrosis. Nature Immunol., 2022. [PubMed]

 

Fibrosis is the result of chronic inflammatory reactions and renal fibrosis. The manifestation of Chronic Kidney Disease (CKD) is the final pathway for end-stage renal failure. Gaining understanding of mechanisms that regulate inflammation is critically important to develop new therapeutics. Additionally, not much is known about basophils’ implication in kidney disease.

 

Doke et al. performed single cell RNA sequencing of over 60K individual cells obtained from mouse models with Unilateral Ureter Obstruction (UUO) surgery, which is an experimental model of kidney fibrosis. They isolated kidneys from 6 sham + 2 UUO mice and identified 8 subclusters of Proximal Tubule (PT) cells, including profibriotic PT cells, based on inflammatory markers. PT fibrotic cells release chemokines that lead to recruitment of lymphoid and myeloid cells. They also demonstrated enrichment of basophils in fibrosis model and predicted the interaction between CXLC1 from PT cells and CXCR2 on basophils. Moreover, IL6 receptor blockage protected mice from renal fibrosis.

 

 

 

 

Figure 2. UMAP plot of 59,609 cells showing 28 distinct cell types identified by unsupervised clustering.

 

 

 

Sepsis: Ulinstatin treatment [↑]

 

 

[3] Chen et al. Integrated Single Cell and Bulk RNA-Seq Analysis Revealed Immunomodulatory Effects of Ulinastatin in Sepsis: A Multicenter Cohort Study. Front. Immunol., 2022. [PubMed]

 

Sepsis is a leading cause of morbidity and mortality in the intensive care unit, and results in uncontrolled inflammatory response due to organ infection. Thus, strenuous effects have been made to develop immunomodulatory drugs, such as ulinastatin (UTI) that showed significant effect on inflammatory biomarkers.

 

Chen et al. used GEXSCOPE® Single Cell RNA Library Kit from Singleron Biotechnologies to explore potential underlying mechanisms of UTI on sepsis by integrating bulk and single cell RNA sequencing from PBMCs. Enrichment analyses, as well as interactome assembly was utilized to provide a comprehensive reference map of transcriptional states of sepsis treated with UTI, as well as a general framework for studying UTI-related mechanisms. They showed that myeloid-derived suppressor cells (MDSCs) are acting as modulatory cells that send more immunosuppressive signals to other cells in the UTI group than the control group. Also, they implicated ANNEXIN in a detrimental role in sepsis, by prolonging neutrophil survival, which is known to contribute to sepsis-mediated organ damage.

 

 

 

Figure 3: UMAP of single cell gene expression profile, stratified by UTI groups. Twelve cell types were identified for the 103,870 cells.

 

 

 

Profiling The Human Dura and Meningioma [↑]

 

 

[4] Wang et al. Single-cell profiling of human dura and meningioma reveals cellular meningeal landscape and insights into meningioma immune response. Genome Medicine, 2022. [PubMed]

 

Recent investigations of the meninges have highlighted the importance of the dura layer in central nervous system immune surveillance beyond a purely structural role. However, our understanding of the meninges largely stems from the use of pre-clinical models rather than human samples.

 

Wang et al. collected the dura and matched tumor from the operating room on ice and performed single cell RNA sequencing with TCR enrichment. They showed that the majority of T cells with highly expanded clonotypes expressed a cytotoxic phenotype in non-tumor-associated dura samples, while tumor-infiltrating T cells were less expanded and did not exhibit a robust cytotoxic phenotype. Additionally, there were shared T cell clonotypes between paired non-tumor-associated dura and meningioma samples. Because meningiomas arise from the dura, this work suggests that tumor-specific T cells could enter meningiomas through the same blood vessels supplying the surrounding non-tumor-associated dura tissue.

 

 

 

Figure 4: (A) Clonal frequency of the dominant TCR, designated by absolute count, and groupings of TCRs ranked by absolute count. (B) UMAP visualization of dura and tumor T cells identified by cell type.

 

 

 

HDAC Inhibitor Therapy in B-cell Lymphoma [↑]

 

 

[5] Wang et al. Single-cell profiling-guided combination therapy of c-Fos and histone deacetylase inhibitors in diffuse large B-cell lymphoma. Clin. Transl. Med., 2022.[PubMed]

 

Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin lymphoma. Histone deacetylase inhibitors (HDACis) have been widely applied in multiple tumours, but the expected efficacy was not observed in DLBCL. Therefore, this study is aimed to explore superior HDACis and optimise a relative combinational therapeutic strategy.

 

Wang et al. used single-cell RNA sequencing (scRNA-Seq) to explore the clonal evolution characteristics of DLBCL cells under treatment pressure with different doses of LAQ824, an HDAC inhibitor. They characterised the heterogeneity of DLBCL cells under different drug pressures, and c-Fos was identified as a critical factor in the survival of residual tumour cells.

 

 

Figure 5: tSNE plot of 11,420 cells labelled by (Left) different concentrations of LAQ824 (n = 4) and (Right) by different cell subtypes (n = 7).

 

 

 

The Tabula Sapiens – Human Single Cell Atlas [↑]

 

 

[6] The Tabula Sapiens Consortium et al. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science, 2022.[PubMed]

 

Cystitis glandularis (CG) usually occurs in chronic inflammation leading to epithelial hyperplasia and metaplasia, which although otherwise benign, could lead to bladder cancer (BLCA) in patients with intestinal metaplasia and urinary tract accumulation.

 

Luo et al. aimed to provide new biological knowledge about the cell composition of CG and the heterogeneity of different grades of bladder cancer. Authors performed single cell RNA sequencing and comprehensively described the expression characteristics of malignant epitheliums and immune cells, as well as the dynamic changes of cell percentages, and the heterogeneity of cell subtypes. They found that a macrophage cluster that highly expressed proinflammatory cytokine TNF, while T cells did not. Another macrophage cluster was shown to highly express immunosuppressive and angiogenic phenotype-related markers that promote tumor progression associated with CD163.

 

 

Figure 6: Changes of cell composition in microenvironment of different bladder samples. (Left) UMAP plot of immune cells and stromal cells, showing different cell types. (Right) T-cell pseudotime development trajectory.

 

 

 

Liver and HBV [↑]

 

 

[7]Zhang al. Single-Cell RNA Transcriptomics Reveals the State of Hepatic Lymphatic Endothelial Cells in Hepatitis B Virus-Related Acute-on-Chronic Liver Failure. Clin. Med., 2022.[PubMed]

 

Retinal drug toxicity screening is essential for the development of safe treatment strategies for many diseases. To this end, retinal organoids derived from human pluripotent stem cells (hPSCs) provide a suitable screening platform due to their similarity to the human retina and the ease of generation in large-scale formats

 

Dorgau et al. aimed to investigate the effectiveness of hPSC-derived organoids on drug testing and validate differentiation by single cell RNA sequencing. They showed that hiPSC cells differentiated to retinal organoids in 150-200 days and tested 6 drugs for toxicity. Drug effects on retinal organoids were comparable to in vivo responses.

 

 

Figure 7: UMAP maps showed 21 transcriptionally distinct cell clusters, comprising all the main retinal cell types together with non-retinal cell clusters, including a proliferating cell and a Fibroblast cell cluster.

 

 

 

Human Placenta Mesenchymal Stem Cells [↑]

 

 

[8] Li et al. Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Mesenchymal Stem/Stromal Cells Derived from Human Placenta. Front. Cell Dev. Biol., 2022.[PubMed]

 

Minimally invasive therapies like microwave ablation (MWA), have been attempted in the treatment of early-stage breast cancer. In situ tumor ablation can create an antigen source and these tumor specific antigens are presented to lymphocytes by dendritic cells and macrophages.

 

Zhou et al. aimed to find key cellular subsets and underlying mechanism of MWA-induced immune response in the treatment of early-stage breast cancer and performed single cell RNA sequencing of PBMC immune profiles from breast cancer patients before and after MWA. They showed that B cells were important antigen-presenting cells (APCs) that initiate CD4+T cells in MWA-induced immune response. The procedure activated CD8+ T cells and increased NK cell cytotoxicity. Also, immune checkpoint inhibitors synergistically activated peripheral T cells after MWA in vitro.

 

 

Figure 8: UMAP analysis of peripheral NK and T cells showing 8 clusters before and after MWA.

 

 

 

Hepatocellular Carcinoma [↑]

 

 

[9] Alvarez et al. Human liver single nucleus and single cell RNA sequencing identify a hepatocellular carcinoma‑associated cell‑type affecting survival. Genome Medicine, 2022.[PubMed]

 

Autoimmune (AI) diseases can affect many organs; however, the prostate has not been considered to be a primary target of these systemic inflammatory processes. Here, Vickman et al. utilized medical record data, patient samples, and in vivo models to evaluate the impact of inflammation, as seen in AI diseases, on prostate tissue. Human and mouse tissues were used to examine whether systemic targeting of inflammation limits prostatic inflammation in benign prostatic hyperplasia (BPH). They implicated BPH T cells and macrophages as sources of TNF and showed that TNF-antagonists (ETANECEPT) reduce prostate hyperplasia and inflammation in NOD mice.

 

 

Figure 9: Workflow scheme and UMAP plot of 69,850 individual cells from 14 patient samples, demonstrating dominant T cell and macrophage populations.

 

 

 

SARSCoV-2 in Monkey Lung vs Intestines [↑]

 

 

[10] Zheng et al. Longitudinal analyses reveal distinct immune response landscapes in lung and intestinal tissues from SARS-CoV-2-infected rhesus macaques. Cell Reports, 2022.[PubMed]

 

Human whipworms (Trichuris trichiura) infect hundreds of millions of people and cause trichuriasis, a major neglected tropical disease with high chronic morbidity and dire socio-economic consequences in affected countries. The molecular mechanisms allowing for the penetration of whipworm larvae to intestinal epithelia are unknown.

 

Duque-Correa et al.  used single cell RNA sequencing to characterize the transcriptomic profiles of whipworm infected mouse caecum and established  Murine caecaloids, the first in-vitro system for whipworm infection and organoid model for live helminths. They revealed that progression of infection results in cell damage and an expansion of enterocytes expressing of Isg15, potentially instigating the host immune response to the whipworm and tissue repair.

 

 

Figure 10: Host IECs responses to early infection with whipworms are dominated by a type-I IFN signature. a Bulk RNA-seq data was analyzed for cell signature genes in the IFN alpha pathway.

 

 

 

References [↑]

 

[1] Sauler et al. Characterization of the COPD alveolar niche using single-cell RNA sequencing. Nat. Commun., 2022. [PubMed]

[2] Doke et al. Single-cell analysis identified the interaction of altered renal tubules with basophils orchestrating kidney fibrosis. Nature Immunol., 2022. [PubMed]

[3] Chen et al. Integrated Single Cell and Bulk RNA-Seq Analysis Revealed Immunomodulatory Effects of Ulinastatin in Sepsis: A Multicenter Cohort Study. Front. Immunol., 2022. [PubMed]

[4] Wang et al. Single-cell profiling of human dura and meningioma reveals cellular meningeal landscape and insights into meningioma immune response. Genome Medicine, 2022. [PubMed]

[5] Wang et al. Single-cell profiling-guided combination therapy of c-Fos and histone deacetylase inhibitors in diffuse large B-cell lymphoma. Clin. Transl. Med., 2022.[PubMed]

[6] The Tabula Sapiens Consortium et al. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science, 2022.[PubMed]

[7] Zhang al. Single-Cell RNA Transcriptomics Reveals the State of Hepatic Lymphatic Endothelial Cells in Hepatitis B Virus-Related Acute-on-Chronic Liver Failure. Clin. Med., 2022.[PubMed]

[8] Li et al. Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Mesenchymal Stem/Stromal Cells Derived from Human Placenta. Front. Cell Dev. Biol., 2022.[PubMed]

[9] Alvarez et al. Human liver single nucleus and single cell RNA sequencing identify a hepatocellular carcinoma‑associated cell‑type affecting survival. Genome Medicine, 2022.[PubMed]

[10] Zheng et al. Longitudinal analyses reveal distinct immune response landscapes in lung and intestinal tissues from SARS-CoV-2-infected rhesus macaques. Cell Reports, 2022.[PubMed]

 

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