Single-Cell High-Resolution Detection and Quantification of Protein Isoforms Differing by a Single Charge Unit

AbstractSingle-cell chromatin studies provide insights into how chromatin structure relates to functions of individual cells. However, balancing high-resolution and genome wide-coverage remains challenging. We describe a computational method for the reconstruction of large 3D-ensembles of single-cell (sc) chromatin conformations from population Hi-C that we apply to study embryogenesis in Drosophila. With minimal assumptions of physical properties and without adjustable parameters, our method generates large ensembles of chromatin conformations via deep-sampling. Our method identifies specific interactions, which constitute 5–6% of Hi-C frequencies, but surprisingly are sufficient to drive chromatin folding, giving rise to the observed Hi-C patterns. Modeled sc-chromatins quantify chromatin heterogeneity, revealing significant changes during embryogenesis. Furthermore, >50% of modeled sc-chromatin maintain topologically associating domains (TADs) in early embryos, when no population TADs are perceptible. Domain boundaries become fixated during development, with strong preference at binding-sites of insulator-complexes upon the midblastula transition. Overall, high-resolution 3D-ensembles of sc-chromatin conformations enable further in-depth interpretation of population Hi-C, improving understanding of the structure-function relationship of genome organization.

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Single-Cell Sequencing: Biological Insight and Potential Clinical Implications in Pediatric Leukemia

Cancers ◽

10.3390/cancers13225658 ◽

2021 ◽

Vol 13 (22) ◽

pp. 5658

Author(s):

Donát Alpár ◽

Bálint Egyed ◽

Csaba Bödör ◽

Gábor T. Kovács

Keyword(s):

High Resolution ◽

Single Cell ◽

Childhood Leukemia ◽

Clinical Decision Making ◽

Cellular Heterogeneity ◽

Therapeutic Interventions ◽

Cell Populations ◽

Pediatric Leukemia ◽

Single Cell Sequencing ◽

Wide Range

Single-cell sequencing (SCS) provides high-resolution insight into the genomic, epigenomic, and transcriptomic landscape of oncohematological malignancies including pediatric leukemia, the most common type of childhood cancer. Besides broadening our biological understanding of cellular heterogeneity, sub-clonal architecture, and regulatory network of tumor cell populations, SCS can offer clinically relevant, detailed characterization of distinct compartments affected by leukemia and identify therapeutically exploitable vulnerabilities. In this review, we provide an overview of SCS studies focused on the high-resolution genomic and transcriptomic scrutiny of pediatric leukemia. Our aim is to investigate and summarize how different layers of single-cell omics approaches can expectedly support clinical decision making in the future. Although the clinical management of pediatric leukemia underwent a spectacular improvement during the past decades, resistant disease is a major cause of therapy failure. Currently, only a small proportion of childhood leukemia patients benefit from genomics-driven therapy, as 15–20% of them meet the indication criteria of on-label targeted agents, and their overall response rate falls in a relatively wide range (40–85%). The in-depth scrutiny of various cell populations influencing the development, progression, and treatment resistance of different disease subtypes can potentially uncover a wider range of driver mechanisms for innovative therapeutic interventions.

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μCB-seq: Microfluidic cell barcoding and sequencing for high-resolution imaging and sequencing of single cells

10.1101/2020.02.18.954974 ◽

2020 ◽

Author(s):

Tyler N. Chen ◽

Anushka Gupta ◽

Mansi Zalavadia ◽

Aaron M. Streets

Keyword(s):

High Resolution ◽

Single Cell ◽

Single Cell Analysis ◽

Protein Localization ◽

Single Cells ◽

Optical Measurements ◽

Detection Sensitivity ◽

High Resolution Imaging ◽

Cell Analysis ◽

Resolution Imaging

AbstractSingle-cell RNA sequencing (scRNA-seq) enables the investigation of complex biological processes in multicellular organisms with high resolution. However, many phenotypic features that are critical to understanding the functional role of cells in a heterogeneous tissue or organ are not directly encoded in the genome and therefore cannot be profiled with scRNA-seq. Quantitative optical microscopy has long been a powerful approach for characterizing diverse cellular phenotypes including cell morphology, protein localization, and chemical composition. Combining scRNA-seq with optical imaging has the potential to provide comprehensive single-cell analysis, allowing for functional integration of gene expression profiling and cell-state characterization. However, it is difficult to track single cells through both measurements; therefore, coupling current scRNA-seq protocols with optical measurements remains a challenge. Here, we report Microfluidic Cell Barcoding and Sequencing (μCB-seq), a microfluidic platform that combines high-resolution imaging and sequencing of single cells. μCB-seq is enabled by a novel fabrication method that preloads primers with known barcode sequences inside addressable reaction chambers of a microfluidic device. In addition to enabling multi-modal single-cell analysis, μCB-seq improves gene detection sensitivity, providing a scalable and accurate method for information-rich characterization of single cells.

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Faculty Opinions recommendation of Time-lapsed, large-volume, high-resolution intravital imaging for tissue-wide analysis of single cell dynamics.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.731183833.793567359 ◽

2019 ◽

Author(s):

Victoria Sanz-Moreno

Keyword(s):

High Resolution ◽

Single Cell ◽

Large Volume ◽

Intravital Imaging ◽

Cell Dynamics

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Synchrotron macro ATR-FTIR microspectroscopy for high-resolution chemical mapping of single cells

The Analyst ◽

10.1039/c8an01543k ◽

2019 ◽

Vol 144 (10) ◽

pp. 3226-3238 ◽

Cited By ~ 27

Author(s):

Jitraporn Vongsvivut ◽

David Pérez-Guaita ◽

Bayden R. Wood ◽

Philip Heraud ◽

Karina Khambatta ◽

...

Keyword(s):

High Resolution ◽

Single Cell ◽

Spatial Resolution ◽

Environmental Science ◽

Single Cell Analysis ◽

Single Cells ◽

Cell Analysis ◽

Chemical Mapping ◽

Ftir Microspectroscopy ◽

Resolution Single

Coupling synchrotron IR beam to an ATR element enhances spatial resolution suited for high-resolution single cell analysis in biology, medicine and environmental science.

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