Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC

Fiškin, Evgenij; Lareau, Caleb A.; Ludwig, Leif S.; Eraslan, Gökçen; Liu, Feimei; Ring, Aaron M.; Xavier, Ramnik J.; Regev, Aviv

doi:10.1038/s41587-021-01065-5

Cited by 41 publications

(31 citation statements)

References 35 publications

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“…Advances in single-cell epigenomics ( 175 ) and multi-omics ( 176 – 178 ) should further enable linking GWAS variants to their target genes and the cell types and programs in which they act. Recent findings indicating that a large fraction of genetic regulatory effects linked to GWAS variants can only be detected at the cellular level ( 11 , 25 ) suggest that cell-level eQTL maps will be essential.…”

Section: Discussionmentioning

confidence: 99%

Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function

Eraslan

Drokhlyansky

Anand

et al. 2022

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Understanding gene function and regulation in homeostasis and disease requires knowledge of the cellular and tissue contexts in which genes are expressed. Here, we applied four single-nucleus RNA sequencing methods to eight diverse, archived, frozen tissue types from 16 donors and 25 samples, generating a cross-tissue atlas of 209,126 nuclei profiles, which we integrated across tissues, donors, and laboratory methods with a conditional variational autoencoder. Using the resulting cross-tissue atlas, we highlight shared and tissue-specific features of tissue-resident cell populations; identify cell types that might contribute to neuromuscular, metabolic, and immune components of monogenic diseases and the biological processes involved in their pathology; and determine cell types and gene modules that might underlie disease mechanisms for complex traits analyzed by genome-wide association studies.

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Section: Discussionmentioning

confidence: 99%

Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function

Eraslan

Drokhlyansky

Anand

et al. 2022

Science

Self Cite

235

224

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“…Single-cell mass spectrometry-based approaches, such as single cell proteomics by mass spectrometry (SCoPE-MS) [51] and SCoPE2 [52], can analyse thousands of proteins and posttranslational modifications in individual cells; however, they have yet to be directly incorporated into a combined multiomics approach. Recently, the PHAGE-ATAC assay [53] demonstrated an alternative approach where antibodies are replaced with nanobody phage-display libraries. This may offer a potential route towards protein detection without the need for antibodies.…”

Section: Linking Transcript and Protein Expressionmentioning

confidence: 99%

“…An overview of current single-cell multiomic approaches. See[12,13,15,16,19,21,22,[24][25][26]28,29,36,41,[45][46][47][48][49][50][53][54][55][56]58,59,61,[63][64][65]102].…”

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confidence: 99%

Into the multiverse: advances in single-cell multiomic profiling

et al. 2022

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“…Recently, Fiskin et al developed a PHAGE-ATAC (Assay for Transposase-Accessible Chromatin) method that uses phage display. Engineered nanobodies (single-domain antibody) measure the single cells protein and chromatin accessibility profile as well as mtDNA-based clonal tracing [ 52 ]. The PHAGE-ATAC was used in multimodal analysis of human immune cells, intracellular protein and detection of SARS-CoV-2 spike protein in human cell population.…”

Section: Signals From Nanomaterials Conjugated With Phagesmentioning

confidence: 99%

Advances in the Development of Phage-Based Probes for Detection of Bio-Species

et al. 2022

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Bacteriophages, abbreviated as “phages”, have been developed as emerging nanoprobes for the detection of a wide variety of biological species, such as biomarker molecules and pathogens. Nanosized phages can display a certain length of exogenous peptides of arbitrary sequence or single-chain variable fragments (scFv) of antibodies that specifically bind to the targets of interest, such as animal cells, bacteria, viruses, and protein molecules. Metal nanoparticles generally have unique plasmon resonance effects. Metal nanoparticles such as gold, silver, and magnetism are widely used in the field of visual detection. A phage can be assembled with metal nanoparticles to form an organic–inorganic hybrid probe due to its nanometer-scale size and excellent modifiability. Due to the unique plasmon resonance effect of this composite probe, this technology can be used to visually detect objects of interest under a dark-field microscope. In summary, this review summarizes the recent advances in the development of phage-based probes for ultra-sensitive detection of various bio-species, outlining the advantages and limitations of detection technology of phage-based assays, and highlighting the commonly used editing technologies of phage genomes such as homologous recombination and clustered regularly interspaced palindromic repeats/CRISPR-associated proteins system (CRISPR-Cas). Finally, we discuss the possible scenarios for clinical application of phage-probe-based detection methods.

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Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC

Cited by 41 publications

References 35 publications

Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function

Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function

Into the multiverse: advances in single-cell multiomic profiling

Advances in the Development of Phage-Based Probes for Detection of Bio-Species

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