Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial-macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.

There is pressing urgency to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2), which causes the disease COVID-19. SARS-CoV-2 spike (S) protein binds angiotensin-converting enzyme 2 (ACE2), and in concert with host proteases, principally transmembrane serine protease 2 (TMPRSS2), promotes cellular entry. The cell subsets targeted by SARS-CoV-2 in host tissues and the factors that regulate ACE2 expression remain unknown. Here, we leverage human, non-human primate, and mouse single-cell RNA-sequencing (scRNA-seq) datasets across health and disease to uncover putative targets of SARS-CoV-2 among tissue-resident cell subsets. We identify ACE2 and TMPRSS2 co-expressing cells within lung type II pneumocytes, ileal absorptive enterocytes, and nasal goblet secretory cells. Strikingly, we discovered that ACE2 is a human interferon-stimulated gene (ISG) in vitro using airway epithelial cells and extend our findings to in vivo viral infections. Our data suggest that SARS-CoV-2 could exploit species-specific interferon-driven upregulation of ACE2, a tissue-protective mediator during lung injury, to enhance infection

Lipid-coated nanocapillaries for DNA sensing

We report a simple and efficient way to accomplish the chemical modification of glass nanopores by means of lipid self-assembly. Lipid coating improves the success rate of these glass nanopores as biosensors to detect lambda-DNA

α_Vβ₃ Integrin-Targeted PLGA-PEG Nanoparticles for Enhanced Anti-tumor Efficacy of a Pt(IV) Prodrug

Targeted delivery of therapeutics to tumor neovasculature is potentially a powerful approach for selective cancer treatment. Integrins are heterodimeric transmembrane proteins involved in cell adhesion and cell signaling, and their expression is commonly upregulated in cancers and inflammatory diseases. The α_vβ₃ integrin is differentially upregulated on angiogenic endothelial cells as well as on many cancer cells. Here we demonstrate the differential targeting of cisplatin prodrug-encapsulated poly(d,l-lactic-<i>co</i>-glycolic acid)-<i>block</i>-polyethylene glycol (PLGA-PEG) nanoparticles (NPs) to the α_vβ₃ integrin on cancer cells using the cyclic pentapeptide c(RGDfK). Cisplatin is one of the most widely used anticancer drugs, and approaches that can improve its therapeutic index are of broad importance. The RGD-targeted Pt(IV)-encapsulated NPs displayed enhanced cytotoxicity as compared to cisplatin administered in its conventional dosage form in model prostate and breast cancer epithelial cells <i>in vitro</i>. Cytotoxicities were also elevated in comparison to those of previously reported systems, a small molecule Pt(IV)-RGD conjugate and a Pt(IV) nanoscale coordination polymer carrying RGD moieties. This result encouraged us also to evaluate the anticancer effect of the new construct in an animal model. The RGD-targeted PLGA-PEG NPs were more efficacious and better tolerated by comparison to cisplatin in an orthotopic human breast cancer xenograft model <i>in vivo</i>

SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues.

There is pressing urgency to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2), which causes the disease COVID-19. SARS-CoV-2 spike (S) protein binds angiotensin-converting enzyme 2 (ACE2), and in concert with host proteases, principally transmembrane serine protease 2 (TMPRSS2), promotes cellular entry. The cell subsets targeted by SARS-CoV-2 in host tissues and the factors that regulate ACE2 expression remain unknown. Here, we leverage human, non-human primate, and mouse single-cell RNA-sequencing (scRNA-seq) datasets across health and disease to uncover putative targets of SARS-CoV-2 among tissue-resident cell subsets. We identify ACE2 and TMPRSS2 co-expressing cells within lung type II pneumocytes, ileal absorptive enterocytes, and nasal goblet secretory cells. Strikingly, we discovered that ACE2 is a human interferon-stimulated gene (ISG) in vitro using airway epithelial cells and extend our findings to in vivo viral infections. Our data suggest that SARS-CoV-2 could exploit species-specific interferon-driven upregulation of ACE2, a tissue-protective mediator during lung injury, to enhance infection

Skin-resident innate lymphoid cells converge on a pathogenic effector state.

Tissue-resident innate lymphoid cells (ILCs) help sustain barrier function and respond to local signals. ILCs are traditionally classified as ILC1, ILC2 or ILC3 on the basis of their expression of specific transcription factors and cytokines1. In the skin, disease-specific production of ILC3-associated cytokines interleukin (IL)-17 and IL-22 in response to IL-23 signalling contributes to dermal inflammation in psoriasis. However, it is not known whether this response is initiated by pre-committed ILCs or by cell-state transitions. Here we show that the&nbsp;induction of psoriasis in mice by IL-23 or imiquimod reconfigures a spectrum of skin ILCs, which converge on a pathogenic ILC3-like state. Tissue-resident ILCs were necessary and sufficient, in the absence of circulatory ILCs, to drive pathology. Single-cell RNA-sequencing (scRNA-seq) profiles of skin ILCs along a time course of psoriatic inflammation formed a dense transcriptional continuum-even at steady state-reflecting fluid ILC states, including a naive or quiescent-like state and an ILC2 effector state. Upon disease induction, the continuum shifted rapidly to span a mixed, ILC3-like subset also expressing cytokines characteristic of ILC2s, which we inferred as arising through multiple trajectories. We confirmed the transition potential of quiescent-like and ILC2 states using in vitro experiments, single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) and in vivo fate mapping. Our results highlight the range and flexibility of skin ILC responses, suggesting that immune activities primed in healthy tissues dynamically adapt to provocations and, left unchecked, drive pathological remodelling

Systematic benchmarking of single-cell ATAC-sequencing protocols.

Acknowledgements: H.H. received support for the project PID2020-115439GB-I00 funded by MCIN/AEI/10.13039/501100011033. This publication is also supported as part of a project (BCLLATLAS and ESPACE) that has received funding from the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement numbers 810287 and 874710). This work was supported by a European Research Council Consolidator grant to S.A. (724226_cis-CONTROL), KU Leuven (C14/22/125 to S.A.), Foundation Against Cancer (F/2020/1396 to S.A.), F.W.O. (grants G0I2722N, G0B5619N and G094121N to S.A. and a PhD fellowship to F.D.) and Aligning Science Across Parkinson’s (grant number ASAP-000430 to S.A.). K.B.M. and S.A.T. are supported by Wellcome (WT211276/Z/18/Z and Sanger core grant WT206194). Computing was performed at the Vlaams Supercomputer Center and high-throughput sequencing at the Genomics Core Leuven. M.R.C. is supported by the National Institutes on Aging K99/R00AG059918. This work was supported by funding from the Rita Allen Foundation (W.J.G.) and the Human Frontiers Science Program (RGY006S; W.J.G.). W.J.G. is a Chan Zuckerberg Biohub investigator and acknowledges grants 2017-174468 and 2018-182817 from the Chan Zuckerberg Initiative and National Institutes of Health grants RM1-HG007735, UM1-HG009442, UM1-HG009436, R01-HG00990901 and U19-AI057266 (to W.J.G.). W.J.G. acknowledges funding from Emerson Collective. B.D. received financial support by Swiss National Science Foundation 310030_197082 and the EPFL. L.S.L. receives support from an Emmy Noether fellowship by the German Research Foundation (LU 2336/2-1), a National Institutes of Health grant UM1HG012076, a Longevity Impetus grant and a Hector Research Career Development Award by the Hector Fellow Academy. A.C.A. is supported by National Institutes of Health grants RF1-MH128842, R35-GM124704 and R01-DA047237 as well as a Silver Family Foundation Innovator Award.Funder: H.H. received support for the project PID2020-115439GB-I00- funded by MCIN/AEI/ 10.13039/501100011033. This publication is also supported as part of a project (BCLLATLAS and ESPACE) that has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement No 810287 and 874710).Funder: M.R.C. is supported by the National Institutes on Aging K99/R00AG059918.Funder: K.B.M. is supported by Wellcome (WT211276/Z/18/Z and Sanger core grant WT206194).Funder: S.A.T. is supported by Wellcome (WT211276/Z/18/Z and Sanger core grant WT206194).Funder: This work was supported by funding from the Rita Allen Foundation (W.J.G.), the Human Frontiers Science (RGY006S) (W.J.G.). W.J.G. is a Chan Zuckerberg Biohub investigator and acknowledges grants 2017-174468 and 2018-182817 from the Chan Zuckerberg Initiative, and the National Institutes of Health grants RM1-HG007735, UM1-HG009442, UM1-HG009436, R01- HG00990901, and U19- AI057266 (to W.J.G.). W.J.G. acknowledges funding from Emerson Collective.Funder: This work was supported by an ERC Consolidator Grant to S.A. (no. 724226_cis- CONTROL), KU Leuven (grant no. C14/22/125 to S.A.), Foundation Against Cancer (grant no, F/2020/1396 to S.A.), F.W.O. (grants G0I2722N, G0B5619N and G094121N to S.A.), Aligning Science Across Parkinson’s (ASAP, grant no. ASAP-000430 to S.A.)Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the performance of eight scATAC-seq methods across 47 experiments using human peripheral blood mononuclear cells (PBMCs) as a reference sample and develop PUMATAC, a universal preprocessing pipeline, to handle the various sequencing data formats. Our analyses reveal significant differences in sequencing library complexity and tagmentation specificity, which impact cell-type annotation, genotype demultiplexing, peak calling, differential region accessibility and transcription factor motif enrichment. Our findings underscore the importance of sample extraction, method selection, data processing and total cost of experiments, offering valuable guidance for future research. Finally, our data and analysis pipeline encompasses 169,000 PBMC scATAC-seq profiles and a best practices code repository for scATAC-seq data analysis, which are freely available to extend this benchmarking effort to future protocols

The ecophysiology of Sprattus sprattus in the Baltic and North Seas

The European sprat (Sprattus sprattus) was a main target species of the German GLOBEC program that investigated the trophodynamic structure and function of the Baltic and North Seas under the influence of physical forcing. This review summarizes literature on the ecophysiology of sprat with an emphasis on describing how environmental factors influence the life-history strategy of this small pelagic fish. Ontogenetic changes in feeding and growth, and the impacts of abiotic and biotic factors on vital rates are discussed with particular emphasis on the role of temperature as a constraint to life-history scheduling of this species in the Baltic Sea. A combination of field and laboratory data suggests that optimal thermal windows for growth and survival change during early life and are wider for eggs (5–17 °C) than in young (8- to 12-mm) early feeding larvae (5–12 °C). As larvae become able to successfully capture larger prey, thermal windows expand to include warmer waters. For example, 12- to 16-mm larvae can grow well at 16 °C and larger, transitional-larvae and early juveniles display the highest rates of feeding and growth at ∼18–22 °C. Gaps in knowledge are identified including the need for additional laboratory studies on the physiology and behavior of larvae (studies that will be particularly critical for biophysical modeling activities) and research addressing the role of overwinter survival as a factor shaping phenology and setting limits on the productivity of this species in areas located at the northern limits of its latitudinal range (such as the Baltic Sea). Based on stage- and temperature-specific mortality and growth potential of early life stages, our analysis suggests that young-of-the year sprat would benefit from inhabiting warmer, near-shore environments rather than the deeper-water spawning grounds such as the Bornholm Basin (central Baltic Sea). Utilization of warmer, nearshore waters (or a general increase in Baltic Sea temperatures) is expected to accelerate growth rates but also enhance the possibility for density-dependent regulation of recruitment (e.g., top-down control of zooplankton resources) acting during the late-larval and juvenile stages, particularly when sprat stocks are at high levels. Highlights ► Field, laboratory and modeling research on the ecophysiology of all sprat life stages is summarized. ► Environmental factors influencing growth and survival are revealed. ► Ontogenetic changes in thermal tolerance and prey requirements constrain life cycle scheduling. ► Gaps in knowledge are identified and future research efforts recommended on sprat recruitment dynamics. ► Exploring seasonal energy allocation will allow a mechanistic understanding of climate impacts

α[subscript v]β[subscript 3] Integrin-Targeted PLGA-PEG Nanoparticles for Enhanced Anti-tumor Efficacy of a Pt(IV) Prodrug

Targeted delivery of therapeutics to tumor neovasculature is potentially a powerful approach for selective cancer treatment. Integrins are heterodimeric transmembrane proteins involved in cell adhesion and cell signaling, and their expression is commonly upregulated in cancers and inflammatory diseases. The α[subscript v]β[subscript 3] integrin is differentially upregulated on angiogenic endothelial cells as well as on many cancer cells. Here we demonstrate the differential targeting of cisplatin prodrug-encapsulated poly(d,l-lactic-co-glycolic acid)-block-polyethylene glycol (PLGA-PEG) nanoparticles (NPs) to the α[subscript v]β[subscript 3] integrin on cancer cells using the cyclic pentapeptide c(RGDfK). Cisplatin is one of the most widely used anticancer drugs, and approaches that can improve its therapeutic index are of broad importance. The RGD-targeted Pt(IV)-encapsulated NPs displayed enhanced cytotoxicity as compared to cisplatin administered in its conventional dosage form in model prostate and breast cancer epithelial cells in vitro. Cytotoxicities were also elevated in comparison to those of previously reported systems, a small molecule Pt(IV)-RGD conjugate and a Pt(IV) nanoscale coordination polymer carrying RGD moieties. This result encouraged us also to evaluate the anticancer effect of the new construct in an animal model. The RGD-targeted PLGA-PEG NPs were more efficacious and better tolerated by comparison to cisplatin in an orthotopic human breast cancer xenograft model in vivo.National Cancer Institute (U.S.) (Grant CA034992