1
|
Abstract
BACKGROUND Heterogeneity in single-cell RNA-seq (scRNA-seq) data is driven by multiple sources, including biological variation in cellular state as well as technical variation introduced during experimental processing. Deconvolving these effects is a key challenge for preprocessing workflows. Recent work has demonstrated the importance and utility of count models for scRNA-seq analysis, but there is a lack of consensus on which statistical distributions and parameter settings are appropriate. RESULTS Here, we analyze 59 scRNA-seq datasets that span a wide range of technologies, systems, and sequencing depths in order to evaluate the performance of different error models. We find that while a Poisson error model appears appropriate for sparse datasets, we observe clear evidence of overdispersion for genes with sufficient sequencing depth in all biological systems, necessitating the use of a negative binomial model. Moreover, we find that the degree of overdispersion varies widely across datasets, systems, and gene abundances, and argues for a data-driven approach for parameter estimation. CONCLUSIONS Based on these analyses, we provide a set of recommendations for modeling variation in scRNA-seq data, particularly when using generalized linear models or likelihood-based approaches for preprocessing and downstream analysis.
Collapse
Affiliation(s)
- Saket Choudhary
- New York Genome Center, 101 Avenue of the Americas, New York, 100013 USA
| | - Rahul Satija
- New York Genome Center, 101 Avenue of the Americas, New York, 100013 USA
- Center for Genomics and Systems Biology, New York University, 12 Waverly Pl, New York, 10003 USA
| |
Collapse
|
2
|
Amiss AS, von Pein JB, Webb JR, Condon ND, Harvey PJ, Phan MD, Schembri MA, Currie BJ, Sweet MJ, Craik DJ, Kapetanovic R, Henriques ST, Lawrence N. Modified horseshoe crab peptides target and kill bacteria inside host cells. Cell Mol Life Sci 2021; 79:38. [PMID: 34971427 PMCID: PMC11071844 DOI: 10.1007/s00018-021-04041-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/09/2021] [Accepted: 11/13/2021] [Indexed: 12/14/2022]
Abstract
Bacteria that occupy an intracellular niche can evade extracellular host immune responses and antimicrobial molecules. In addition to classic intracellular pathogens, other bacteria including uropathogenic Escherichia coli (UPEC) can adopt both extracellular and intracellular lifestyles. UPEC intracellular survival and replication complicates treatment, as many therapeutic molecules do not effectively reach all components of the infection cycle. In this study, we explored cell-penetrating antimicrobial peptides from distinct structural classes as alternative molecules for targeting bacteria. We identified two β-hairpin peptides from the horseshoe crab, tachyplesin I and polyphemusin I, with broad antimicrobial activity toward a panel of pathogenic and non-pathogenic bacteria in planktonic form. Peptide analogs [I11A]tachyplesin I and [I11S]tachyplesin I maintained activity toward bacteria, but were less toxic to mammalian cells than native tachyplesin I. This important increase in therapeutic window allowed treatment with higher concentrations of [I11A]tachyplesin I and [I11S]tachyplesin I, to significantly reduce intramacrophage survival of UPEC in an in vitro infection model. Mechanistic studies using bacterial cells, model membranes and cell membrane extracts, suggest that tachyplesin I and polyphemusin I peptides kill UPEC by selectively binding and disrupting bacterial cell membranes. Moreover, treatment of UPEC with sublethal peptide concentrations increased zinc toxicity and enhanced innate macrophage antimicrobial pathways. In summary, our combined data show that cell-penetrating peptides are attractive alternatives to traditional small molecule antibiotics for treating UPEC infection, and that optimization of native peptide sequences can deliver effective antimicrobials for targeting bacteria in extracellular and intracellular environments.
Collapse
Affiliation(s)
- Anna S Amiss
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jessica B von Pein
- Institute for Molecular Bioscience, IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jessica R Webb
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, NT, 0811, Australia
| | - Nicholas D Condon
- Australian Cancer Research Foundation/Institute for Molecular Bioscience Cancer Biology Imaging Facility, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peta J Harvey
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Minh-Duy Phan
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, The University of Queensland, Queensland, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, The University of Queensland, Queensland, Australia
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, NT, 0811, Australia
- Department of Infectious Diseases and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, NT, 0811, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience, IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ronan Kapetanovic
- Institute for Molecular Bioscience, IMB Centre for Inflammation and Disease Research and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, 4072, Australia.
- Friedrich Miescher Institute for Biomedical Research, 4058, Basel, BS, Switzerland.
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia.
- Queensland University of Technology, School of Biomedical Sciences, Translational Research Institute, Brisbane, QLD, 4102, Australia.
| | - Nicole Lawrence
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD, 4072, Australia.
| |
Collapse
|